3LZA

Crystal structure of Putative SnoaL-like polyketide cyclase (YP_563807.1) from SHEWANELLA DENITRIFICANS OS-217 at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3LZA/pdb

• Classification: LYASE
• Organism(s): Shewanella denitrificans OS217
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-01 Released: 2010-05-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

CRYSTAL STRUCTURE OF PUTATIVE SNOAL-LIKE POLYKETIDE CYCLASE (YP_563807.1) FROM SHEWANELLA DENITRIFICANS OS-217 AT 1.70 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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.19 kDa 
• Atom Count: 5,149 
• Modelled Residue Count: 547 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative SnoaL-like polyketide cyclase	A, B, C, D	141	Shewanella denitrificans OS217	Mutation(s): 0  Gene Names: YP_563807.1, Sden_2805
UniProt
Find proteins for Q12KE2 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12KE2  Go to UniProtKB:  Q12KE2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M33LZA

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.843	α = 90.13
b = 56.51	β = 103.27
c = 57.537	γ = 102.85

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  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