3F9S | pdb_00003f9s

Crystal structure of a putative polyketide cyclase (lferr_0659) from acidithiobacillus ferrooxidans atcc at 1.76 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3F9S/pdb

• Classification: LYASE
• Organism(s): Acidithiobacillus ferrooxidans ATCC 23270
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-14 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: 1.76 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Crystal structure of putative polyketide cyclase (AFE_2539) from ACIDITHIOBACILLUS FERROOXIDANS NCIB8455 at 1.76 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: 33.17 kDa 
• Atom Count: 2,635 
• Modeled Residue Count: 285 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative polyketide cyclase	A, B	146	Acidithiobacillus ferrooxidans ATCC 23270	Mutation(s): 0  Gene Names: AFE_2539, Lferr_0659

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 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: 1.76 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33F9S

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.97	α = 90
b = 48.594	β = 94.19
c = 55.967	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: 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: Advisory, Version format compliance
• Version 1.2: 2014-04-02
  Changes: Source and taxonomy
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.6: 2024-11-27
  Changes: Data collection, Structure summary