5XNK | pdb_00005xnk

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.217 (Depositor), 0.229 (DCC)
R-Value Work:
0.179 (Depositor), 0.188 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RNB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2AS Query on 2AS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2S,3S)-3-methyl-aspartic acid C₅ H₉ N O₄ LXRUAYBIUSUULX-HRFVKAFMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACB Query on ACB Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3-METHYL-BETA-D-ASPARTIC ACID C₅ H₉ N O₄ LXRUAYBIUSUULX-STHAYSLISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.217 (Depositor), 0.229 (DCC)
R-Value Work: 0.179 (Depositor), 0.188 (DCC)
R-Value Observed: 0.181 (Depositor)

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

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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

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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.