3HHL | pdb_00003hhl

Crystal structure of methylated RPA0582 protein

PDB DOI: https://doi.org/10.2210/pdb3HHL/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Rhodopseudomonas palustris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-15 Released: 2009-07-07
Deposition Author(s): Sledz, P., Niedzialkowska, E., Chruszcz, M., Porebski, P., Yim, V., Kudritska, M., Zimmerman, M.D., Evdokimova, E., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.206 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of methylated RPA0582 protein

Sledz, P., Niedzialkowska, E., Chruszcz, M., Porebski, P., Yim, V., Kudritska, M., Zimmerman, M.D., Evdokimova, E., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 69.5 kDa
Atom Count: 4,944
Modeled Residue Count: 540
Deposited Residue Count: 572
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RPA0582	A	143	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: RPA0582
UniProt
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90 Go to UniProtKB: Q6NC90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NC90
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RPA0582	B	143	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: RPA0582
UniProt
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90 Go to UniProtKB: Q6NC90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NC90
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RPA0582	C	143	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: RPA0582
UniProt
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90 Go to UniProtKB: Q6NC90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NC90
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RPA0582	D	143	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: RPA0582
UniProt
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90 Go to UniProtKB: Q6NC90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NC90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain J [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain J [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain J [auth A]	EA [auth D], J [auth A]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain J [auth A] Interactions & Density Focus chain EA [auth D] Focus chain J [auth A]
PE8 Query on PE8 Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C]	R [auth B], Z [auth C]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain R [auth B] Focus chain Z [auth C]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain W [auth C]	CA [auth D], W [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain W [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain Y [auth C] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth C]	I [auth A], Q [auth B], Y [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth B] Focus chain Y [auth C] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B] Focus chain Y [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C]	DA [auth D] H [auth A] K [auth A] N [auth B] O [auth B] DA [auth D], H [auth A], K [auth A], N [auth B], O [auth B], P [auth B], X [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain H [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain H [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain U [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain U [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain U [auth C]	E [auth A], F [auth A], U [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain U [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain U [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth D] SDF format, chain L [auth A] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B]	AA [auth C], FA [auth D], L [auth A], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain L [auth A] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain L [auth A] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain V [auth C]	BA [auth D], G [auth A], M [auth B], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain G [auth A] Focus chain M [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain G [auth A] Focus chain M [auth B] Focus chain V [auth C]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MLZ Query on MLZ	A	L-PEPTIDE LINKING	C₇ H₁₆ N₂ O₂		LYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.206 (Depositor), 0.220 (DCC)
R-Value Work: 0.178 (Depositor), 0.190 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.012	α = 90
b = 193.012	β = 90
c = 117.965	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-02-01
Changes: Database references
Version 1.4: 2023-09-20
Changes: Data collection, Refinement description
Version 1.5: 2023-11-22
Changes: Data collection