3F7X | pdb_00003f7x

Crystal structure of a putative polyketide cyclase (pp0894) from pseudomonas putida kt2440 at 1.24 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3F7X/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-10 Released: 2008-11-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.122 (Depositor) 

Literature

Crystal structure of Putative polyketide cyclase. (NP_743055.1) from PSEUDOMONAS PUTIDA KT2440 at 1.24 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)

Macromolecule Content 

• Total Structure Weight: 17.75 kDa 
• Atom Count: 1,380 
• Modeled Residue Count: 133 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative polyketide cyclase	A	151	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: NP_743055.1, PP0894, PP_0894
UniProt
Find proteins for Q88PF6 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88PF6  Go to UniProtKB:  Q88PF6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	B [auth A], C [auth A]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-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: 1.24 Å
• R-Value Free:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.122 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33F7X

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.762	α = 90
b = 74.985	β = 118.03
c = 36.543	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: 2008-11-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: 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: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary