4J9W | pdb_00004j9w

Crystal structure of the complex of a hydroxyproline epimerase (TARGET EFI-506499, PSEUDOMONAS FLUORESCENS PF-5) with the inhibitor pyrrole-2-carboxylate

• PDB DOI: https://doi.org/10.2210/pdb4J9W/pdb

• Classification: Isomerase/Isomerase Inhibitor complex
• Organism(s): Pseudomonas protegens Pf-5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-02-17 Released: 2013-03-13 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.232 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of a hydroxyproline epimerase (TARGET EFI-506499, PSEUDOMONAS FLUORESCENS PF-5) with the inhibitor pyrrole-2-carboxylate

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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: 72.62 kDa 
• Atom Count: 5,301 
• Modeled Residue Count: 620 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline racemase family protein	A, B	332	Pseudomonas protegens Pf-5	Mutation(s): 0  Gene Names: PFL_1412 EC: 5.1.1.8
UniProt
Find proteins for Q4KGU2 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4KGU2  Go to UniProtKB:  Q4KGU2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYC	D [auth A], H [auth B]	PYRROLE-2-CARBOXYLATE C5 H4 N O2 WRHZVMBBRYBTKZ-UHFFFAOYSA-M
GOL	C [auth A], F [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.232 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.174	α = 90
b = 74.637	β = 105.46
c = 87.048	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description