3G79 | pdb_00003g79

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.296 (Depositor), 0.292 (DCC)
R-Value Work:
0.222 (Depositor), 0.218 (DCC)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3G79

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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 (PDB Primary Data), 1.1.1.336 (UniProt)
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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8PXR2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.296 (Depositor), 0.292 (DCC)
R-Value Work: 0.222 (Depositor), 0.218 (DCC)
R-Value Observed: 0.225 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2009-02-17

Deposition Author(s):

Malashkevich, V.N.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

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

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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.