2PWZ | pdb_00002pwz

Crystal structure of the apo form of E.Coli malate dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb2PWZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Mutation(s): No

Deposited: 2007-05-14 Released: 2007-05-29
Deposition Author(s): Soderberg, C.A.G., Clarke, T.A., Richardson, D.J., Hemmings, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.246 (Depositor), 0.240 (DCC)
R-Value Work:
0.199 (Depositor), 0.195 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

The X-ray crystal structure of the apo form of E.Coli malate dehydrogenase in space group C2

Soderberg, C.A.G., Clarke, T.A., Richardson, D.J., Hemmings, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 129.47 kDa
Atom Count: 9,470
Modeled Residue Count: 1,244
Deposited Residue Count: 1,248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B [auth C], C [auth E], D [auth G]	312	Escherichia coli K-12	Mutation(s): 0 EC: 1.1.1.37
UniProt
Find proteins for P61889 (Escherichia coli (strain K12)) Explore P61889 Go to UniProtKB: P61889
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61889
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.246 (Depositor), 0.240 (DCC)
R-Value Work: 0.199 (Depositor), 0.195 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.466	α = 90
b = 52.485	β = 102.28
c = 170.2	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

Soderberg, C.A.G.

Richardson, D.J.

Revision History (Full details and data files)

Version 1.0: 2007-05-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description

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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.