4OW1

Crystal Structure of Resuscitation Promoting Factor C

PDB DOI: https://doi.org/10.2210/pdb4OW1/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-01-29 Released: 2014-06-18
Deposition Author(s): Chauviac, F.X., Quay, D.H.X., Cohen-Gonsaud, M., Keep, N.H.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), FRISBI, European Union (EU), Bloomsbury Studentship, Commonwealth Study Commision

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.235
R-Value Work: 0.205
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain.

Chauviac, F.X., Robertson, G., Quay, D.H., Bagneris, C., Dumas, C., Henderson, B., Ward, J., Keep, N.H., Cohen-Gonsaud, M.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1022-1026

PubMed: 25084374 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X1401317X
Primary Citation of Related Structures:
4OW1

PubMed Abstract:
The first structure of the catalytic domain of RpfC (Rv1884), one of the resuscitation-promoting factors (RPFs) from Mycobacterium tuberculosis, is reported. The structure was solved using molecular replacement once the space group had been correctly identified as twinned P21 rather than the apparent C2221 by searching for anomalous scattering sites in P1. The structure displays a very high degree of structural conservation with the previously published structures of the catalytic domains of RpfB (Rv1009) and RpfE (Rv2450). This structural conservation highlights the importance of the versatile domain composition of the RPF family.

Organizational Affiliation

Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, England.

Macromolecule Content

Total Structure Weight: 74.63 kDa
Atom Count: 5,002
Modelled Residue Count: 665
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Resuscitation-promoting factor RpfC	A B C [auth E] D [auth X] E [auth W] A, B, C [auth E], D [auth X], E [auth W], F [auth T], G [auth S], H [auth U]	92	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: MTCY180.34, Rv1884c, rpfC EC: 3
UniProt
Find proteins for O07747 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O07747 Go to UniProtKB: O07747
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O07747
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth W] MOL2 format, chain I [auth A] MOL2 format, chain J [auth W]	I [auth A], J [auth W]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth W] Interactions & Density Focus chain I [auth A] Focus chain J [auth W]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.235
R-Value Work: 0.205
R-Value Observed: 0.207
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.23	α = 90
b = 89.93	β = 115.08
c = 78.09	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2014-06-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	G0401038
FRISBI	France	ANR-10-INSB-05-01
European Union (EU)	European Union	X-TB
Bloomsbury Studentship	United Kingdom	FXC
Commonwealth Study Commision	United Kingdom	MYCS-2011-252

Revision History (Full details and data files)

Version 1.0: 2014-06-18
Type: Initial release
Version 1.1: 2014-08-13
Changes: Database references
Version 1.2: 2015-02-04
Changes: Derived calculations
Version 1.3: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
Version 1.4: 2020-01-08
Changes: Author supporting evidence
Version 1.5: 2023-12-27
Changes: Data collection, Database references, Refinement description