7PB3

Structural and Functional analysis of the Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii

• PDB DOI: https://doi.org/10.2210/pdb7PB3/pdb

• Classification: ISOMERASE
• Organism(s): Acetoanaerobium sticklandii DSM 519
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-30 Released: 2022-08-10 
• Deposition Author(s): Najmudin, S., Pan, X.-S., McAuley, K.E., Fisher, L.M., Sanderson, M.R.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.330 
• R-Value Work: 0.251 

Starting Model: experimental

Literature

Structural and Functional analysis of the Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii

Najmudin, S., Pan, X.-S., McAuley, K.E., Fisher, L.M., Sanderson, M.R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.1 kDa 
• Atom Count: 5,186 
• Modelled Residue Count: 670 
• Deposited Residue Count: 686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline racemase A (AsProR)	A [auth AAA], B [auth BBB]	343	Acetoanaerobium sticklandii DSM 519	Mutation(s): 0  Gene Names: prdF, CLOST_2228 EC: 5.1.1.4
UniProt
Find proteins for E3PTZ4 (Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF)) Explore E3PTZ4  Go to UniProtKB:  E3PTZ4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYC (Subject of Investigation/LOI)	C [auth AAA], D [auth BBB]	PYRROLE-2-CARBOXYLATE C5 H4 N O2 WRHZVMBBRYBTKZ-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.330 
• R-Value Work: 0.251 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.041	α = 90
b = 109.041	β = 90
c = 105.163	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
STARANISO	data scaling
DIALS	data scaling
MoRDa	phasing
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Najmudin, S., Pan, X.-S., McAuley, K.E., Fisher, L.M., Sanderson, M.R.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/T000848/1

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description