3LMX | pdb_00003lmx

Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis

PDB DOI: https://doi.org/10.2210/pdb3LMX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-02-01 Released: 2011-02-16
Deposition Author(s): Purpero, V.M., Lipscomb, J.D., Shi, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis

Purpero, V.M., Lipscomb, J.D., Ohlendorf, D.H., Shi, K., Dolbeare, K.B., Brown, C.K., Burk, D.

To be published.

Macromolecule Content

Total Structure Weight: 151.93 kDa
Atom Count: 11,263
Modeled Residue Count: 1,314
Deposited Residue Count: 1,314
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocatechuate 3,4-dioxygenase alpha chain	A, C [auth B], E [auth C]	200	Pseudomonas putida	Mutation(s): 0 Gene Names: pcaG EC: 1.13.11.3
UniProt
Find proteins for P00436 (Pseudomonas putida) Explore P00436 Go to UniProtKB: P00436
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00436
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocatechuate 3,4-dioxygenase beta chain	B [auth M], D [auth N], F [auth O]	238	Pseudomonas putida	Mutation(s): 1 Gene Names: pcaH EC: 1.13.11.3
UniProt
Find proteins for P00437 (Pseudomonas putida) Explore P00437 Go to UniProtKB: P00437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00437
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DHB Query on DHB Download Ideal Coordinates CCD File SDF format, chain DB [auth O] SDF format, chain JA [auth N] SDF format, chain KA [auth N] SDF format, chain P [auth M] SDF format, chain Q [auth M] SDF format, chain R [auth M] MOL2 format, chain DB [auth O] MOL2 format, chain JA [auth N] MOL2 format, chain KA [auth N] MOL2 format, chain P [auth M] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] mmCIF format, chain DB [auth O] mmCIF format, chain JA [auth N] mmCIF format, chain KA [auth N] mmCIF format, chain P [auth M] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M]	DB [auth O] JA [auth N] KA [auth N] P [auth M] Q [auth M] DB [auth O], JA [auth N], KA [auth N], P [auth M], Q [auth M], R [auth M]	3,4-DIHYDROXYBENZOIC ACID C₇ H₆ O₄ YQUVCSBJEUQKSH-UHFFFAOYSA-N		Interactions Focus chain DB [auth O] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain P [auth M] Focus chain Q [auth M] Focus chain R [auth M] Interactions & Density Focus chain DB [auth O] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain P [auth M] Focus chain Q [auth M] Focus chain R [auth M]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain FB [auth O] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain NA [auth N] SDF format, chain PA [auth N] SDF format, chain V [auth M] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain FB [auth O] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain NA [auth N] MOL2 format, chain PA [auth N] MOL2 format, chain V [auth M] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain FB [auth O] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain NA [auth N] mmCIF format, chain PA [auth N] mmCIF format, chain V [auth M] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	FB [auth O] GA [auth B] H [auth A] I [auth A] NA [auth N] FB [auth O], GA [auth B], H [auth A], I [auth A], NA [auth N], PA [auth N], V [auth M], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FB [auth O] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain NA [auth N] Focus chain PA [auth N] Focus chain V [auth M] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain FB [auth O] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain NA [auth N] Focus chain PA [auth N] Focus chain V [auth M] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain JB [auth O] SDF format, chain LA [auth N] SDF format, chain MA [auth N] SDF format, chain OA [auth N] SDF format, chain S [auth M] SDF format, chain T [auth M] SDF format, chain U [auth M] SDF format, chain UA [auth N] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain JB [auth O] MOL2 format, chain LA [auth N] MOL2 format, chain MA [auth N] MOL2 format, chain OA [auth N] MOL2 format, chain S [auth M] MOL2 format, chain T [auth M] MOL2 format, chain U [auth M] MOL2 format, chain UA [auth N] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain JB [auth O] mmCIF format, chain LA [auth N] mmCIF format, chain MA [auth N] mmCIF format, chain OA [auth N] mmCIF format, chain S [auth M] mmCIF format, chain T [auth M] mmCIF format, chain U [auth M] mmCIF format, chain UA [auth N]	FA [auth B] G [auth A] JB [auth O] LA [auth N] MA [auth N] FA [auth B], G [auth A], JB [auth O], LA [auth N], MA [auth N], OA [auth N], S [auth M], T [auth M], U [auth M], UA [auth N]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain G [auth A] Focus chain JB [auth O] Focus chain LA [auth N] Focus chain MA [auth N] Focus chain OA [auth N] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth M] Focus chain UA [auth N] Interactions & Density Focus chain FA [auth B] Focus chain G [auth A] Focus chain JB [auth O] Focus chain LA [auth N] Focus chain MA [auth N] Focus chain OA [auth N] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth M] Focus chain UA [auth N]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain BA [auth M] SDF format, chain BB [auth C] SDF format, chain CA [auth M] SDF format, chain DA [auth M] SDF format, chain EA [auth M] SDF format, chain EB [auth O] SDF format, chain GB [auth O] SDF format, chain HA [auth B] SDF format, chain HB [auth O] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KB [auth O] SDF format, chain LB [auth O] SDF format, chain M [auth A] SDF format, chain MB [auth O] SDF format, chain N [auth A] SDF format, chain QA [auth N] SDF format, chain RA [auth N] SDF format, chain TA [auth N] SDF format, chain VA [auth N] SDF format, chain W [auth M] SDF format, chain X [auth M] SDF format, chain Z [auth M] MOL2 format, chain BA [auth M] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth M] MOL2 format, chain DA [auth M] MOL2 format, chain EA [auth M] MOL2 format, chain EB [auth O] MOL2 format, chain GB [auth O] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth O] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth O] MOL2 format, chain LB [auth O] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth O] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth N] MOL2 format, chain RA [auth N] MOL2 format, chain TA [auth N] MOL2 format, chain VA [auth N] MOL2 format, chain W [auth M] MOL2 format, chain X [auth M] MOL2 format, chain Z [auth M] mmCIF format, chain BA [auth M] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth M] mmCIF format, chain DA [auth M] mmCIF format, chain EA [auth M] mmCIF format, chain EB [auth O] mmCIF format, chain GB [auth O] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth O] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth O] mmCIF format, chain LB [auth O] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth O] mmCIF format, chain N [auth A] mmCIF format, chain QA [auth N] mmCIF format, chain RA [auth N] mmCIF format, chain TA [auth N] mmCIF format, chain VA [auth N] mmCIF format, chain W [auth M] mmCIF format, chain X [auth M] mmCIF format, chain Z [auth M]	BA [auth M] BB [auth C] CA [auth M] DA [auth M] EA [auth M] BA [auth M], BB [auth C], CA [auth M], DA [auth M], EA [auth M], EB [auth O], GB [auth O], HA [auth B], HB [auth O], J [auth A], K [auth A], KB [auth O], LB [auth O], M [auth A], MB [auth O], N [auth A], QA [auth N], RA [auth N], TA [auth N], VA [auth N], W [auth M], X [auth M], Z [auth M]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain BA [auth M] Focus chain BB [auth C] Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth M] Focus chain EB [auth O] Focus chain GB [auth O] Focus chain HA [auth B] Focus chain HB [auth O] Focus chain J [auth A] Focus chain K [auth A] Focus chain KB [auth O] Focus chain LB [auth O] Focus chain M [auth A] Focus chain MB [auth O] Focus chain N [auth A] Focus chain QA [auth N] Focus chain RA [auth N] Focus chain TA [auth N] Focus chain VA [auth N] Focus chain W [auth M] Focus chain X [auth M] Focus chain Z [auth M] Interactions & Density Focus chain BA [auth M] Focus chain BB [auth C] Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth M] Focus chain EB [auth O] Focus chain GB [auth O] Focus chain HA [auth B] Focus chain HB [auth O] Focus chain J [auth A] Focus chain K [auth A] Focus chain KB [auth O] Focus chain LB [auth O] Focus chain M [auth A] Focus chain MB [auth O] Focus chain N [auth A] Focus chain QA [auth N] Focus chain RA [auth N] Focus chain TA [auth N] Focus chain VA [auth N] Focus chain W [auth M] Focus chain X [auth M] Focus chain Z [auth M]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain CB [auth O] SDF format, chain IA [auth N] SDF format, chain O [auth M] MOL2 format, chain CB [auth O] MOL2 format, chain IA [auth N] MOL2 format, chain O [auth M] mmCIF format, chain CB [auth O] mmCIF format, chain IA [auth N] mmCIF format, chain O [auth M]	CB [auth O], IA [auth N], O [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain CB [auth O] Focus chain IA [auth N] Focus chain O [auth M] Interactions & Density Focus chain CB [auth O] Focus chain IA [auth N] Focus chain O [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain AB [auth C] SDF format, chain IB [auth O] SDF format, chain L [auth A] SDF format, chain SA [auth N] SDF format, chain Y [auth M] MOL2 format, chain AA [auth M] MOL2 format, chain AB [auth C] MOL2 format, chain IB [auth O] MOL2 format, chain L [auth A] MOL2 format, chain SA [auth N] MOL2 format, chain Y [auth M] mmCIF format, chain AA [auth M] mmCIF format, chain AB [auth C] mmCIF format, chain IB [auth O] mmCIF format, chain L [auth A] mmCIF format, chain SA [auth N] mmCIF format, chain Y [auth M]	AA [auth M] AB [auth C] IB [auth O] L [auth A] SA [auth N] AA [auth M], AB [auth C], IB [auth O], L [auth A], SA [auth N], Y [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth M] Focus chain AB [auth C] Focus chain IB [auth O] Focus chain L [auth A] Focus chain SA [auth N] Focus chain Y [auth M] Interactions & Density Focus chain AA [auth M] Focus chain AB [auth C] Focus chain IB [auth O] Focus chain L [auth A] Focus chain SA [auth N] Focus chain Y [auth M]