4LMR | pdb_00004lmr

Crystal structure of L-lactate dehydrogenase from Bacillus cereus ATCC 14579, NYSGRC Target 029452

PDB DOI: https://doi.org/10.2210/pdb4LMR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus cereus ATCC 14579
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-10 Released: 2013-07-31
Deposition Author(s): Malashkevich, V.N., Bonanno, J.B., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.179 (Depositor), 0.190 (DCC)
R-Value Work:
0.163 (Depositor), 0.172 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of L-lactate dehydrogenase from Bacillus cereus ATCC 14579, NYSGRC Target 029452

Malashkevich, V.N., Bonanno, J.B., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 75.52 kDa
Atom Count: 4,997
Modeled Residue Count: 624
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase 1	A, B	336	Bacillus cereus ATCC 14579	Mutation(s): 0 Gene Names: BC_1924, ldh, ldh1 EC: 1.1.1.27
UniProt
Find proteins for Q81EP4 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81EP4 Go to UniProtKB: Q81EP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q81EP4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.179 (Depositor), 0.190 (DCC)
R-Value Work: 0.163 (Depositor), 0.172 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.276	α = 90
b = 177.276	β = 90
c = 168.975	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-07-31

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-07-31
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-10-16
Changes: Structure summary