5XNJ

Crystal structure of Microcystis aeruginosa PCC 7806 aspartate/glutamate racemase in complex with L-glutamate

PDB DOI: https://doi.org/10.2210/pdb5XNJ/pdb

Classification: ISOMERASE
Organism(s): Microcystis aeruginosa PCC 7806
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-05-23 Released: 2018-05-30
Deposition Author(s): Cao, D.D., Zhou, K., Jiang, Y.L., Zhou, C.Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.210
R-Value Work: 0.187
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure-function Analyses of a Cyanobacterial Aspartate/Glutamate Racemase Reveal Its Catalytic Mechanism and Substrate Specificity

Cao, D.D., Zhou, C.Z.

To be published.

Macromolecule Content

Total Structure Weight: 29.36 kDa
Atom Count: 1,809
Modelled Residue Count: 227
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
McyF	A	260	Microcystis aeruginosa PCC 7806	Mutation(s): 2 Gene Names: mcyF, IPF_371
UniProt
Find proteins for Q9RNB4 (Microcystis aeruginosa (strain PCC 7806)) Explore Q9RNB4 Go to UniProtKB: Q9RNB4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RNB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.210
R-Value Work: 0.187
R-Value Observed: 0.188
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.247	α = 90
b = 129.247	β = 90
c = 44.292	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-05-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-30
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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 R01GM133198.