2RIL | pdb_00002ril

Crystal structure of a putative monooxygenase (YP_001095275.1) from Shewanella loihica PV-4 at 1.26 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2RIL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Shewanella loihica PV-4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-11 Released: 2007-10-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.162 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Literature

Crystal structure of A Putative Monooxygenase (YP_001095275.1) from Shewanella loihica PV-4 at 1.26 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 11.46 kDa 
• Atom Count: 937 
• Modeled Residue Count: 95 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibiotic biosynthesis monooxygenase	A	99	Shewanella loihica PV-4	Mutation(s): 0  Gene Names: YP_001095275.1, Shew_3150
UniProt
Find proteins for A3QHR8 (Shewanella loihica (strain ATCC BAA-1088 / PV-4)) Explore A3QHR8  Go to UniProtKB:  A3QHR8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGO	D [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.162 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32RIL

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.931	α = 90
b = 63.155	β = 90
c = 27.283	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary