3HHP | pdb_00003hhp

Malate dehydrogenase open conformation

PDB DOI: https://doi.org/10.2210/pdb3HHP/pdb

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

Deposited: 2009-05-15 Released: 2009-09-22
Deposition Author(s): Zaitseva, J., Meneely, K.M., Lamb, A.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.214 (Depositor), 0.211 (DCC)
R-Value Work:
0.186 (Depositor), 0.183 (DCC)
R-Value Observed:
0.188 (Depositor)

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This is version 1.2 of the entry. See complete history.

Literature

Structure of Escherichia coli malate dehydrogenase at 1.45 A resolution.

Zaitseva, J., Meneely, K.M., Lamb, A.L.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 866-869

PubMed: 19724119 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309109032217
Primary Citation Related Structures:
3HHP

PubMed Abstract:
The structure of apo malate dehydrogenase from Escherichia coli has been determined to 1.45 A resolution. The crystals belonged to space group C2, with unit-cell parameters a = 146.0, b = 52.0, c = 168.9 A, beta = 102.2 degrees. The structure was determined with the molecular-replacement pipeline program BALBES and was refined to a final R factor of 18.6% (R(free) = 21.4%). The final model has two dimers in the asymmetric unit. In each dimer one monomer contains the active-site loop in the open conformation, whereas in the opposing monomer the active-site loop is disordered.

Organizational Affiliation

Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA.

Macromolecule Content

Total Structure Weight: 129.47 kDa
Atom Count: 9,989
Modeled Residue Count: 1,234
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, C, D	312	Escherichia coli K-12	Mutation(s): 0 Gene Names: mdh, b3236, JW3205 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: 1.45 Å
R-Value Free: 0.214 (Depositor), 0.211 (DCC)
R-Value Work: 0.186 (Depositor), 0.183 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.026	α = 90
b = 51.972	β = 102.23
c = 168.98	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
BALBES	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-09-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 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.