3F8H

Crystal structure of a putative polyketide cyclase (tm1040_3560) from silicibacter sp. tm1040 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3F8H/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Ruegeria sp. TM1040
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-12 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: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Crystal structure of putative polyketide cyclase (YP_611791.1) from SILICIBACTER SP. TM1040 at 2.00 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: 35.26 kDa 
• Atom Count: 2,510 
• Modelled Residue Count: 274 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative polyketide cyclase	A, B	150	Ruegeria sp. TM1040	Mutation(s): 0  Gene Names: TM1040_3560, YP_611791.1
UniProt
Find proteins for Q1GLD7 (Ruegeria sp. (strain TM1040)) Explore Q1GLD7  Go to UniProtKB:  Q1GLD7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	G [auth A], L [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 2.00 Å
• R-Value Free: 0.213 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33F8H

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.31	α = 90
b = 63.31	β = 90
c = 196.09	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: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  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