3LOV

Crystal structure of Putative protoporphyrinogen oxidase (YP_001813199.1) from Exiguobacterium sp. 255-15 at 2.06 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Putative protoporphyrinogen oxidase (YP_001813199.1) from Exiguobacterium sp. 255-15 at 2.06 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protoporphyrinogen oxidase
A
475Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15)Mutation(s): 0 
EC: 1.3.3.4
Find proteins for B1YKJ9 (Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15))
Go to UniProtKB:  B1YKJ9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-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

Unit Cell:
Length (Å)Angle (°)
a = 74.542α = 90.00
b = 74.542β = 90.00
c = 212.559γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
PHENIXrefinement
SHELXphasing
SHELXDphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
MolProbitymodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description