3AJ3

Crystal structure of selenomethionine substituted 4-pyridoxolactonase from Mesorhizobium loti


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.577 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of 4-pyridoxolactonase from Mesorhizobium loti

Kobayashi, J.Yoshikane, Y.Yagi, T.Baba, S.Mizutani, K.Takahashi, N.Mikami, B.

(2014) Acta Crystallogr.,Sect.F 70: 424-432


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-pyridoxolactonase
A
274Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)Mutation(s): 0 
EC: 3.1.1.27
Find proteins for Q988B9 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099))
Go to UniProtKB:  Q988B9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.577 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.777α = 90.00
b = 39.214β = 117.92
c = 84.191γ = 90.00
Software Package:
Software NamePurpose
SHELXEmodel building
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
RESOLVEphasing
HKL-2000data collection
RESOLVEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-04-09
    Type: Database references