3LOV | pdb_00003lov

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

• PDB DOI: https://doi.org/10.2210/pdb3LOV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Exiguobacterium artemiae 255-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-04 Released: 2010-02-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.7 kDa 
• Atom Count: 3,904 
• Modeled Residue Count: 451 
• Deposited Residue Count: 475 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protoporphyrinogen oxidase	A	475	Exiguobacterium artemiae 255-15	Mutation(s): 0  Gene Names: Exig_0701 EC: 1.3.3.4 (PDB Primary Data), 1.3.3.15 (UniProt)
UniProt
Find proteins for B1YKJ9 (Exiguobacterium sibiricum (strain DSM 17290 / CCUG 55495 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YKJ9  Go to UniProtKB:  B1YKJ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LOV

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.542	α = 90
b = 74.542	β = 90
c = 212.559	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary