2DY3

Crystal Structure of alanine racemase from Corynebacterium glutamicum

PDB DOI: https://doi.org/10.2210/pdb2DY3/pdb

Classification: ISOMERASE
Organism(s): Corynebacterium glutamicum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-09-05 Released: 2007-09-11
Deposition Author(s): Miyaguchi, I., Sasaki, C., Kato, R., Oikawa, T., Sugio, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.269
R-Value Work: 0.227

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Alanine Racemase from Corynebacterium glutamicum at 2.1 A resolution

Miyaguchi, I., Sasaki, C., Kato, R., Oikawa, T., Sugio, S.

To be published.

Macromolecule Content

Total Structure Weight: 157.87 kDa
Atom Count: 11,220
Modelled Residue Count: 1,365
Deposited Residue Count: 1,444
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase	A, B, C, D	361	Corynebacterium glutamicum	Mutation(s): 0 Gene Names: alr EC: 5.1.1.1
UniProt
Find proteins for Q8RSU9 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8RSU9 Go to UniProtKB: Q8RSU9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RSU9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.269
R-Value Work: 0.227
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.384	α = 90
b = 113.612	β = 94.73
c = 88.096	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-09-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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2DY3

Crystal Structure of alanine racemase from Corynebacterium glutamicum

Crystal Structure of Alanine Racemase from Corynebacterium glutamicum at 2.1 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)