3FI9 | pdb_00003fi9

Crystal structure of malate dehydrogenase from Porphyromonas gingivalis

PDB DOI: https://doi.org/10.2210/pdb3FI9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Porphyromonas gingivalis ATCC 33277
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-12-11 Released: 2008-12-23
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Miller, S., Romero, R., Wasserman, S., 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: 1.90 Å
R-Value Free:
0.295 (Depositor), 0.280 (DCC)
R-Value Work:
0.252 (Depositor), 0.242 (DCC)
R-Value Observed:
0.254 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3FI9

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

Literature

Crystal structure of malate dehydrogenase from Porphyromonas gingivalis

Bonanno, J.B., Freeman, J., Bain, K.T., Miller, S., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 74.61 kDa
Atom Count: 5,211
Modeled Residue Count: 641
Deposited Residue Count: 686
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B	343	Porphyromonas gingivalis ATCC 33277	Mutation(s): 0 Gene Names: PGN_1880
UniProt
Find proteins for B2RM04 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)) Explore B2RM04 Go to UniProtKB: B2RM04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2RM04
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.295 (Depositor), 0.280 (DCC)
R-Value Work: 0.252 (Depositor), 0.242 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.385	α = 90
b = 74.133	β = 90
c = 135.296	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-12-23

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-12-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, 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.