4OH1

Crystal structure of a putative zinc-binding dehydrogenase (gutB) from Clostridium scindens ATCC 35704 at 2.00 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb4OH1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): [Clostridium] scindens ATCC 35704
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-16 Released: 2014-02-05 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.216 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Literature

Crystal structure of a putative zinc-binding dehydrogenase (gutB) from Clostridium scindens ATCC 35704 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.12 kDa 
• Atom Count: 2,918 
• Modelled Residue Count: 351 
• Deposited Residue Count: 351 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-iditol 2-dehydrogenase	A	351	[Clostridium] scindens ATCC 35704	Mutation(s): 0  Gene Names: CLOSCI_00901, gutB, ZP_02430688, gutB_2, HDCHBGLK_00843 EC: 1.1.1.14 (PDB Primary Data), 1.1.1.1 (UniProt)
UniProt
Find proteins for B0NC68 (Clostridium scindens (strain ATCC 35704 / DSM 5676 / VPI 13733 / 19)) Explore B0NC68  Go to UniProtKB:  B0NC68

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	G [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.216 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: I 2 2 2
• Diffraction Data: https://doi.org/10.18430/M34OH1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.87	α = 90
b = 85.597	β = 90
c = 149.087	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-05 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations