4G2P | pdb_00004g2p

Crystal structure of peptidyl-prolyl cis-trans isomerase domain II of molecular chaperone SurA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

• PDB DOI: https://doi.org/10.2210/pdb4G2P/pdb

• Classification: ISOMERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-12 Released: 2012-08-01 
• Deposition Author(s): Chang, C., Wu, R., Adkins, J.N., Brown, R.N., Cort, J.R., Heffron, F., Nakayasu, E.S., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of peptidyl-prolyl cis-trans isomerase domain II of molecular chaperone SurA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Chang, C., Wu, R., Adkins, J.N., Brown, R.N., Cort, J.R., Heffron, F., Nakayasu, E.S., Jedrzejczak, R., Joachimiak, A.

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 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: 24.42 kDa 
• Atom Count: 1,899 
• Modeled Residue Count: 216 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone SurA	A, B	110	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S	Mutation(s): 0  Gene Names: surA, STM14_0111 EC: 5.2.1.8
UniProt
Find proteins for A0A0F6AWM7 (Salmonella typhimurium (strain 14028s / SGSC 2262)) Explore A0A0F6AWM7  Go to UniProtKB:  A0A0F6AWM7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A]	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: 1.82 Å
• R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.499	α = 90
b = 39.611	β = 101.7
c = 68.581	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Chang, C., Wu, R., Adkins, J.N., Brown, R.N., Cort, J.R., Heffron, F., Nakayasu, E.S., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-10-16
  Changes: Structure summary