2GUG | pdb_00002gug

NAD-dependent formate dehydrogenase from Pseudomonas sp.101 in complex with formate

• PDB DOI: https://doi.org/10.2210/pdb2GUG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas sp. 101
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-04-30 Released: 2006-05-16 
• Deposition Author(s): Filippova, E.V., Polyakov, K.M., Tikhonova, T.V., Boiko, K.M., Tishkov, V.I., Popov, V.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of NAD-dependent formate dehydrogenase from metylotrophic bacterium Pseudomonas sp.101 with formate.

Filippova, E.V., Polyakov, K.M., Tikhonova, T.V., Stekhanova, T.N., Boiko, K.M., Sadihov, I.G., Tishkov, V.I., Labrou, N., Popov, V.O.

(2006) Кристаллография 51: 663-667

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 178.13 kDa 
• Atom Count: 11,994 
• Modeled Residue Count: 1,468 
• Deposited Residue Count: 1,604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B, C, D	401	Pseudomonas sp. 101	Mutation(s): 1  EC: 1.2.1.2 (PDB Primary Data), 1.17.1.9 (UniProt)
UniProt
Find proteins for P33160 (Pseudomonas sp. (strain 101)) Explore P33160  Go to UniProtKB:  P33160

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth A], O [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	G [auth A], H [auth A], I [auth A], K [auth B], M [auth C], N [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
FMT	F [auth A], J [auth B], L [auth C]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117	α = 90
b = 54.98	β = 95.74
c = 128.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MARHKL	data reduction
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-16 
Deposition Author(s): Filippova, E.V., Polyakov, K.M., Tikhonova, T.V., Boiko, K.M., Tishkov, V.I., Popov, V.O.

Revision History  

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection