4Q2H | pdb_00004q2h

Crystal structure of probable proline racemase from agrobacterium radiobacter K84, TARGET EFI-506561, with bound carbonate

• PDB DOI: https://doi.org/10.2210/pdb4Q2H/pdb

• Classification: ISOMERASE
• Organism(s): Rhizobium rhizogenes K84
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-08 Released: 2014-04-30 
• Deposition Author(s): Patskovsky, Y., 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., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.176 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Proline Racemase Arad_0731 from Agrobacterium Radiobacter, Target Efi-506561

Patskovsky, Y., 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., 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: 79.03 kDa 
• Atom Count: 5,878 
• Modeled Residue Count: 686 
• Deposited Residue Count: 734 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline racemase protein	A, B	367	Rhizobium rhizogenes K84	Mutation(s): 0  Gene Names: Arad_0731 EC: 5.1.1.8
UniProt
Find proteins for B9J8G8 (Rhizobium rhizogenes (strain K84 / ATCC BAA-868)) Explore B9J8G8  Go to UniProtKB:  B9J8G8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT	C [auth A], E [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.176 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.43	α = 90
b = 129.47	β = 90
c = 178.703	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Patskovsky, Y., 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., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-04-30
  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: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary