5CVC

Structure of maize serine racemase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine racemaseA, B, C346Zea maysMutation(s): 0 
UniProt
Find proteins for F5CAQ9 (Zea mays)
Explore F5CAQ9 
Go to UniProtKB:  F5CAQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5CAQ9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.992α = 90
b = 204.017β = 90
c = 211.847γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
MrBUMPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Advisory, Derived calculations