4Q60 | pdb_00004q60

Crystal structure of a 4-hydroxyproline epimerase from Burkholderia Multivorans atcc 17616, target EFI-506586, open form, with bound pyrrole-2-carboxylate

• PDB DOI: https://doi.org/10.2210/pdb4Q60/pdb

• Classification: ISOMERASE
• Organism(s): Burkholderia multivorans ATCC 17616
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-18 Released: 2014-05-07 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Sojitra, S., Stead, M., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF PROLINE RACEMASE Bmul_4447 FROM Burkholderia multivorans, TARGET EFI-506586

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Sojitra, S., Stead, M., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., 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: 71.04 kDa 
• Atom Count: 5,143 
• Modeled Residue Count: 621 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROLINE RACEMASE	A, B	332	Burkholderia multivorans ATCC 17616	Mutation(s): 0  Gene Names: BMUL_4447 EC: 5.1.1.4 (PDB Primary Data), 5.1.1.8 (UniProt)
UniProt
Find proteins for B3D6W2 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore B3D6W2  Go to UniProtKB:  B3D6W2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYC	D [auth A], E [auth B]	PYRROLE-2-CARBOXYLATE C5 H4 N O2 WRHZVMBBRYBTKZ-UHFFFAOYSA-M
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.749	α = 90
b = 95.053	β = 90
c = 126.275	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Sojitra, S., Stead, M., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary