4JUU | pdb_00004juu

Crystal structure of a putative hydroxyproline epimerase from xanthomonas campestris (TARGET EFI-506516) with bound phosphate and unknown ligand

• PDB DOI: https://doi.org/10.2210/pdb4JUU/pdb

• Classification: ISOMERASE
• Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-25 Released: 2013-04-17 
• 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: 1.75 Å
• R-Value Free: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative hydroxyproline epimerase from xanthomonas campestris (TARGET EFI-506516) with bound phosphate and unknown ligand

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: 71.12 kDa 
• Atom Count: 5,287 
• Modeled Residue Count: 626 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epimerase	A, B	334	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 0  Gene Names: XCC2415 EC: 5.1.1.8
UniProt
Find proteins for Q8P833 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P833  Go to UniProtKB:  Q8P833

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL	I [auth B]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.893	α = 90
b = 108.749	β = 90
c = 116.204	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: 2013-04-17 
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: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description