4E21 | pdb_00004e21

The crystal structure of 6-phosphogluconate dehydrogenase from Geobacter metallireducens

PDB DOI: https://doi.org/10.2210/pdb4E21/pdb

Classification: OXIDOREDUCTASE
Organism(s): Geobacter metallireducens GS-15
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-07 Released: 2012-03-21
Deposition Author(s): Zhang, Z., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.239 (Depositor), 0.232 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of 6-phosphogluconate dehydrogenase from Geobacter metallireducens

Zhang, Z., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 79.85 kDa
Atom Count: 5,003
Modeled Residue Count: 628
Deposited Residue Count: 716
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase (Decarboxylating)	A, B	358	Geobacter metallireducens GS-15	Mutation(s): 0 Gene Names: Gmet_2620 EC: 1.1.1.44
UniProt
Find proteins for Q39SD5 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)) Explore Q39SD5 Go to UniProtKB: Q39SD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q39SD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.239 (Depositor), 0.232 (DCC)
R-Value Work: 0.195 (Depositor), 0.195 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.297	α = 90
b = 184.832	β = 90
c = 93.496	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-03-21
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary