2WFI | pdb_00002wfi

Atomic resolution crystal structure of the PPIase domain of human cyclophilin G

• PDB DOI: https://doi.org/10.2210/pdb2WFI/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-06 Released: 2009-06-16 
• Deposition Author(s): Stegmann, C.M., Sheldrick, G.M., Wahl, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.75 Å
• R-Value Free: 
  0.124 (Depositor), 0.117 (DCC) 
• R-Value Observed: 
  0.107 (Depositor) 

Literature

The Thermodynamic Influence of Trapped Water Molecules on a Protein-Ligand Interaction

Stegmann, C.M., Seeliger, D., Sheldrick, G.M., De Groot, B.L., Wahl, M.C.

(2009) Angew Chem Int Ed Engl 48: 5207

• PubMed: 19499554 
• DOI: https://doi.org/10.1002/anie.200900481
• Primary Citation Related Structures: 
  2WFI, 2WFJ


• PubMed Abstract: 
  

  Water molecules doing time: Atomic-resolution crystal structures of the PPIase domain of cyclophilin G, alone and in complex with cyclosporin A, and together with MD simulations and calorimetry, reveal how trapped water molecules influence the thermodynamic profile of a protein-ligand interaction.

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Organizational Affiliation: 
• Research Group X-ray Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

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: 19.94 kDa 
• Atom Count: 1,920 
• Modeled Residue Count: 172 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE G	A	179	Homo sapiens	Mutation(s): 0  EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13427 (Homo sapiens) Explore Q13427  Go to UniProtKB:  Q13427
PHAROS:  Q13427 GTEx:  ENSG00000138398

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.75 Å
• R-Value Free:  0.124 (Depositor), 0.117 (DCC) 
• R-Value Observed: 0.107 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.544	α = 90
b = 65.144	β = 90
c = 69.68	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Stegmann, C.M., Sheldrick, G.M., Wahl, M.C.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-22
  Changes: Data collection, Derived calculations, Other, Refinement description
• Version 1.4: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary