7PB3 | pdb_00007pb3

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free:
0.330 (Depositor), 0.331 (DCC)
R-Value Work:
0.251 (Depositor), 0.250 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7PB3

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E3PTZ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PYC (Subject of Investigation/LOI) Query on PYC Download:Ideal Coordinates CCD File SDF format, chain D [auth BBB] SDF format, chain C [auth AAA] MOL2 format, chain D [auth BBB] MOL2 format, chain C [auth AAA] mmCIF format, chain D [auth BBB] mmCIF format, chain C [auth AAA]	C [auth AAA], D [auth BBB]	PYRROLE-2-CARBOXYLATE C₅ H₄ N O₂ WRHZVMBBRYBTKZ-UHFFFAOYSA-M		Interactions Focus chain C [auth AAA] Focus chain D [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.330 (Depositor), 0.331 (DCC)
R-Value Work: 0.251 (Depositor), 0.250 (DCC)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-10

Deposition Author(s):

Sanderson, M.R.

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

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.