4QTP | pdb_00004qtp

Crystal Structure of an Anti-sigma Factor Antagonist from Mycobacterium paratuberculosis

PDB DOI: https://doi.org/10.2210/pdb4QTP/pdb

Classification: PROTEIN BINDING
Organism(s): Mycobacterium avium subsp. paratuberculosis K-10
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-08 Released: 2014-07-16
Deposition Author(s): Dranow, D.M., Clifton, M.C., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.193 (Depositor), 0.200 (DCC)
R-Value Work:
0.166 (Depositor), 0.176 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of an Anti-sigma Factor Antagonist from Mycobacterium paratuberculosis

Dranow, D.M., Clifton, M.C., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 61.79 kDa
Atom Count: 3,904
Modeled Residue Count: 465
Deposited Residue Count: 576
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-sigma factor antagonist	A, B, C, D	144	Mycobacterium avium subsp. paratuberculosis K-10	Mutation(s): 0 Gene Names: MAP_0380
UniProt
Find proteins for Q744G1 (Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10)) Explore Q744G1 Go to UniProtKB: Q744G1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q744G1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain U [auth D]	E [auth A], J [auth B], N [auth C], U [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain U [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain X [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain X [auth D] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain X [auth D]	I [auth A], M [auth B], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain H [auth A]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.193 (Depositor), 0.200 (DCC)
R-Value Work: 0.166 (Depositor), 0.176 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.17	α = 69.66
b = 58.3	β = 78.61
c = 58.9	γ = 78.94

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2025-10-22
Changes: Structure summary