4LB0 | pdb_00004lb0

Crystal structure of a hydroxyproline epimerase from agrobacterium vitis, target efi-506420, with bound trans-4-oh-l-proline

• PDB DOI: https://doi.org/10.2210/pdb4LB0/pdb

• Classification: ISOMERASE
• Organism(s): Allorhizobium ampelinum S4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-20 Released: 2013-07-17 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Hammonds, J., 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: 1.70 Å
• R-Value Free: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a hydroxyproline epimerase from agrobacterium vitis, target efi-506420, with bound trans-4-oh-l-proline

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Hammonds, J., 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: 74.85 kDa 
• Atom Count: 5,918 
• Modeled Residue Count: 689 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	348	Allorhizobium ampelinum S4	Mutation(s): 0  Gene Names: Avi_0518 EC: 5.1.1.8
UniProt
Find proteins for B9JQV3 (Allorhizobium ampelinum (strain ATCC BAA-846 / DSM 112012 / S4)) Explore B9JQV3  Go to UniProtKB:  B9JQV3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HYP	E [auth B]	4-HYDROXYPROLINE C5 H9 N O3 PMMYEEVYMWASQN-DMTCNVIQSA-N
ACT	C [auth A], D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.014	α = 90
b = 178.014	β = 90
c = 49.735	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: 2013-07-17 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Hammonds, J., 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: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description