3I0Y

Crystal structure of a putative polyketide cyclase (xcc0381) from xanthomonas campestris pv. campestris at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3I0Y/pdb

• Classification: ISOMERASE
• Organism(s): Xanthomonas campestris pv. campestris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-25 Released: 2009-07-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

Crystal structure of putative polyketide cyclase (NP_635776.1) from XANTHOMONAS CAMPESTRIS at 1.50 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

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 64.28 kDa 
• Atom Count: 5,148 
• Modelled Residue Count: 545 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative polyketide cyclase	A, B, C, D	140	Xanthomonas campestris pv. campestris	Mutation(s): 0  Gene Names: NP_635776.1, XCC0381
UniProt
Find proteins for Q8PDF7 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8PDF7  Go to UniProtKB:  Q8PDF7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A], K [auth B], L [auth B], Q [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	E [auth A], F [auth A], I [auth B], J [auth B], N [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL	H [auth A], M [auth B], O [auth C], R [auth D]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.50 Å
• R-Value Free: 0.206 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M33I0Y

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.627	α = 90
b = 98.776	β = 110.45
c = 62.053	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary