3S6M | pdb_00003s6m

The structure of a Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3S6M/pdb

• Classification: ISOMERASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-25 Released: 2011-06-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.183 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

The structure of a Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei

Clifton, M.C., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.49 kDa 
• Atom Count: 1,432 
• Modeled Residue Count: 163 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A	167	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: BURPS1710b_2684 EC: 5.2.1.8
UniProt
Find proteins for Q3JQT3 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JQT3  Go to UniProtKB:  Q3JQT3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.183 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33S6M

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.657	α = 90
b = 80.657	β = 90
c = 43.338	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description