5XNK

Crystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with DL-methyl-aspartate

• PDB DOI: https://doi.org/10.2210/pdb5XNK/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.217 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

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

Cao, D.D., Zhou, C.Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.52 kDa 
• Atom Count: 1,810 
• Modelled Residue Count: 227 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
McyF	A	260	Microcystis aeruginosa PCC 7806	Mutation(s): 1  Gene Names: mcyF, IPF_371
UniProt
Find proteins for Q9RNB4 (Microcystis aeruginosa (strain PCC 7806)) Explore Q9RNB4  Go to UniProtKB:  Q9RNB4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACB	C [auth A]	3-METHYL-BETA-D-ASPARTIC ACID C5 H9 N O4 LXRUAYBIUSUULX-STHAYSLISA-N
2AS	B [auth A]	(2S,3S)-3-methyl-aspartic acid C5 H9 N O4 LXRUAYBIUSUULX-HRFVKAFMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.217 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.046	α = 90
b = 129.046	β = 90
c = 43.898	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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