5V8T | pdb_00005v8t

Crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354

• PDB DOI: https://doi.org/10.2210/pdb5V8T/pdb

• Classification: ISOMERASE
• Organism(s): Saccharomyces cerevisiae S288C, Burkholderia pseudomallei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-22 Released: 2018-03-14 
• Deposition Author(s): Lorimer, D.D., Dranow, D.M., Seufert, F., Abendroth, J., Holzgrabe, U.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354

Lorimer, D.D., Dranow, D.M., Seufert, F., Abendroth, J., Holzgrabe, U.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.97 kDa 
• Atom Count: 3,202 
• Modeled Residue Count: 382 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase	A, B	208	Saccharomyces cerevisiae S288C, Burkholderia pseudomallei This entity is chimeric	Mutation(s): 0  Gene Names: SMT3, YDR510W, D9719.15, fbp_2, DP46_4351, DP49_3058, ERS012314_03208, SY87_03945 EC: 5.2.1.8
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306  Go to UniProtKB:  Q12306
Find proteins for Q63J95 (Burkholderia pseudomallei (strain K96243)) Explore Q63J95  Go to UniProtKB:  Q63J95
UniProt Groups	Q12306Q63J95

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8ZV	C [auth A], E [auth B]	2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate C28 H38 N2 O9 S SJJQRFSCVQPRPK-SANMLTNESA-N
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35v8t

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.64	α = 90
b = 32.5	β = 96.73
c = 99.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Lorimer, D.D., Dranow, D.M., Seufert, F., Abendroth, J., Holzgrabe, U.

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Data collection
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description