4GBJ | pdb_00004gbj

Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans

PDB DOI: https://doi.org/10.2210/pdb4GBJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Dyadobacter fermentans DSM 18053
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-07-27 Released: 2012-09-05
Deposition Author(s): Michalska, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.197 (Depositor), 0.201 (DCC)
R-Value Work:
0.160 (Depositor)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans

Michalska, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 128.77 kDa
Atom Count: 9,154
Modeled Residue Count: 1,158
Deposited Residue Count: 1,188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase NAD-binding	A, B, C, D	297	Dyadobacter fermentans DSM 18053	Mutation(s): 0 Gene Names: Dfer_3638
UniProt
Find proteins for C6VV20 (Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114)) Explore C6VV20 Go to UniProtKB: C6VV20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6VV20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain E [auth B] MOL2 format, chain F [auth C] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain E [auth B] mmCIF format, chain F [auth C] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain E [auth B]	E [auth B], F [auth C], G [auth C], H [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.197 (Depositor), 0.201 (DCC)
R-Value Work: 0.160 (Depositor)
R-Value Observed: 0.161 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.633	α = 90
b = 89.645	β = 90
c = 151.506	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
BUCCANEER	model building
Coot	model building
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
BUCCANEER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2012-09-05
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.