3QPE | pdb_00003qpe

Crystal structure of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with D-Galacturonate and 5-keto-4-deoxy-D-Galacturonate

PDB DOI: https://doi.org/10.2210/pdb3QPE/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Paenibacillus sp. Y412MC10
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-02-12 Released: 2012-02-15
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.270 (Depositor), 0.270 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with D-Galacturonate and 5-keto-4-deoxy-D-Galacturonate

Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 176.7 kDa
Atom Count: 12,829
Modeled Residue Count: 1,517
Deposited Residue Count: 1,568
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B, C, D	392	Paenibacillus sp. Y412MC10	Mutation(s): 0 Gene Names: GYMC10_3367
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGU Query on DGU Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	D-galacturonic acid C₆ H₁₀ O₇ IAJILQKETJEXLJ-RSJOWCBRSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
D54 Query on D54 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	J [auth B], M [auth C], Q [auth D]	4-deoxy-L-threo-hex-5-ulosuronic acid C₆ H₈ O₆ IMUGYKFHMJLTOU-UCORVYFPSA-N		Interactions Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain K [auth C]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], O [auth D], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.270 (Depositor), 0.270 (DCC)
R-Value Work: 0.221 (Depositor), 0.220 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.019	α = 90
b = 66.265	β = 95.73
c = 154.609	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-15
Type: Initial release
Version 2.0: 2020-07-01
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description