3G79

Crystal structure of NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase from Methanosarcina mazei Go1

• PDB DOI: https://doi.org/10.2210/pdb3G79/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanosarcina mazei Go1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-09 Released: 2009-02-17 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.296 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Crystal structure of NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase from Methanosarcina mazei Go1

Malashkevich, V.N., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

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 (software)

Macromolecule Content

• Total Structure Weight: 103.97 kDa 
• Atom Count: 7,421 
• Modelled Residue Count: 950 
• Deposited Residue Count: 956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase	A, B	478	Methanosarcina mazei Go1	Mutation(s): 0  Gene Names: MM_1154 EC: 1.1.1
UniProt
Find proteins for Q8PXR2 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PXR2  Go to UniProtKB:  Q8PXR2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.296 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.83	α = 90
b = 88.723	β = 90
c = 151.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references