5CVC

Structure of maize serine racemase

• PDB DOI: https://doi.org/10.2210/pdb5CVC/pdb

• Classification: ISOMERASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-26 Released: 2016-03-16 
• Deposition Author(s): Song, Y., Zou, L., Fan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of maize serine racemase with pyridoxal 5'-phosphate.

Zou, L., Song, Y., Wang, C., Sun, J., Wang, L., Cheng, B., Fan, J.

(2016) Acta Crystallogr F Struct Biol Commun 72: 165-171

• PubMed: 26919519 
• DOI: https://doi.org/10.1107/S2053230X16000960
• Primary Citation of Related Structures:  
  5CVC


• PubMed Abstract: 
  

  Serine racemase (SR) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that is responsible for D-serine biosynthesis in vivo. The first X-ray crystal structure of maize SR was determined to 2.1 Å resolution and PLP binding was confirmed in solution by UV-Vis absorption spectrometry. Maize SR belongs to the type II PLP-dependent enzymes and differs from the SR of a vancomycin-resistant bacterium. The PLP is bound to each monomer by forming a Schiff base with Lys67. Structural comparison with rat and fission yeast SRs reveals a similar arrangement of active-site residues but a different orientation of the C-terminal helix.

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Organizational Affiliation: 

School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, People's Republic of China.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.06 kDa 
• Atom Count: 7,265 
• Modelled Residue Count: 965 
• Deposited Residue Count: 1,038 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine racemase	A, B, C	346	Zea mays	Mutation(s): 0
UniProt
Find proteins for F5CAQ9 (Zea mays) Explore F5CAQ9  Go to UniProtKB:  F5CAQ9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], G [auth B], I [auth C]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MG	D [auth A], F [auth B], H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.992	α = 90
b = 204.017	β = 90
c = 211.847	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
MrBUMP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Song, Y., Zou, L., Fan, J.

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Advisory, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description