5AQC | pdb_00005aqc

KstR, transcriptional repressor of cholesterol degradation in Mycobacterium tuberculosis, bound to the cholesterol coenzyme A derivative, (25R)-3-oxocholest-4-en-26-oyl-CoA.

PDB DOI: https://doi.org/10.2210/pdb5AQC/pdb

Classification: TRANSCRIPTION
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-21 Released: 2016-10-05
Deposition Author(s): Podust, L.M., Ouellet, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.226 (Depositor), 0.221 (DCC)
R-Value Work:
0.184 (Depositor), 0.189 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Kstr, Transcriptional Repressor of Cholesterol Degradation in Mycobacterium Tuberculosis, Bound to the Cholesterol Coenzyme a Derivative, (25S)-3- Oxocholest-4-En-26-Oyl-Coa.

Podust, L.M., Ouellet, H.

To be published.

Macromolecule Content

Total Structure Weight: 48.4 kDa
Atom Count: 3,111
Modeled Residue Count: 364
Deposited Residue Count: 410
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-TYPE TRANSCRIPTIONAL REPRESSOR KSTR	A, B	205	Mycobacterium tuberculosis H37Rv	Mutation(s): 0
UniProt
Find proteins for P96856 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P96856 Go to UniProtKB: P96856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P96856
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5JB Query on 5JB Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	(25S)-3-oxocholest-4-en-26-oyl-CoA C₄₈ H₇₆ N₇ O₁₈ P₃ S QHTNQHCVKNUPEI-ZAXAEIALSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.226 (Depositor), 0.221 (DCC)
R-Value Work: 0.184 (Depositor), 0.189 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.329	α = 90
b = 67.404	β = 105.71
c = 49.923	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Podust, L.M.

Ouellet, H.

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

5AQC | pdb_00005aqc

KstR, transcriptional repressor of cholesterol degradation in Mycobacterium tuberculosis, bound to the cholesterol coenzyme A derivative, (25R)-3-oxocholest-4-en-26-oyl-CoA.

Literature

Kstr, Transcriptional Repressor of Cholesterol Degradation in Mycobacterium Tuberculosis, Bound to the Cholesterol Coenzyme a Derivative, (25S)-3- Oxocholest-4-En-26-Oyl-Coa.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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