3KY8 | pdb_00003ky8

Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KY8/pdb

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


• Deposited: 2009-12-04 Released: 2009-12-22 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 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 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 45.75 kDa 
• Atom Count: 3,119 
• Modeled Residue Count: 361 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative riboflavin biosynthesis protein	A, B	197	Shewanella loihica PV-4	Mutation(s): 0  Gene Names: Shew_0776
UniProt
Find proteins for A3QB00 (Shewanella loihica (strain ATCC BAA-1088 / PV-4)) Explore A3QB00  Go to UniProtKB:  A3QB00

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNL	C [auth A], D [auth A], H [auth B], I [auth B]	Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33KY8

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.679	α = 90
b = 72.679	β = 90
c = 156.974	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: 2009-12-22 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, 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: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary