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- PDB-5cxi: Crystal structure of Mycobacterium tuberculosis KstR in complex w... -

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Basic information

Entry
Database: PDB / ID: 5cxi
TitleCrystal structure of Mycobacterium tuberculosis KstR in complex with 3-oxo-23,24-bisnorchol-4-en-22-oyl-CoA (4-BNC-CoA)
ComponentsHTH-type transcriptional repressor KstR
KeywordsTRANSCRIPTION / Transcriptional repressor / TetR family Tcholesterol catabolism / CoA thioester ligand / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding
Similarity search - Function
HTH-type transcriptional repressor KstR, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-oxo-23,24-bisnorchol-4-en-22-oyl-CoA / HTH-type transcriptional repressor KstR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHo, N.A.T. / Dawes, S. / Kendall, S. / Casabon, I. / Crowe, A.M. / Baker, E.N. / Eltis, L.D. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC)
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC)12/1111 New Zealand
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Structure of the Transcriptional Repressor KstR in Complex with CoA Thioester Cholesterol Metabolites Sheds Light on the Regulation of Cholesterol Catabolism in Mycobacterium tuberculosis.
Authors: Ho, N.A. / Dawes, S.S. / Crowe, A.M. / Casabon, I. / Gao, C. / Kendall, S.L. / Baker, E.N. / Eltis, L.D. / Lott, J.S.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional repressor KstR
B: HTH-type transcriptional repressor KstR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8934
Polymers44,7052
Non-polymers2,1882
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-15 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.777, 67.264, 124.234
Angle α, β, γ (deg.)90.00, 96.79, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

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Components

#1: Protein HTH-type transcriptional repressor KstR


Mass: 22352.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: kstR, Rv3574 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P96856
#2: Chemical ChemComp-5TW / 3-oxo-23,24-bisnorchol-4-en-22-oyl-CoA


Mass: 1094.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H66N7O18P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES/imidazole pH 6.5, 10% PEG 4000, 20% glycerol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassiuml L-tartrate, 0.02 M sodium oxamate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→47.88 Å / Num. obs: 27478 / % possible obs: 99.6 % / Redundancy: 8.3 % / Net I/av σ(I): 9.5 / Net I/σ(I): 0.19
Reflection shellResolution: 2→2.05 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.042 / Mean I/σ(I) obs: 3.4 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.831 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2752 1350 4.91 %
Rwork0.2429 --
obs0.2446 27469 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 61 225 2940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012964
X-RAY DIFFRACTIONf_angle_d0.6143752
X-RAY DIFFRACTIONf_dihedral_angle_d12.945968
X-RAY DIFFRACTIONf_chiral_restr0.03450
X-RAY DIFFRACTIONf_plane_restr0.003472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.34091290.30152590X-RAY DIFFRACTION99
2.0715-2.15440.29941210.27122578X-RAY DIFFRACTION99
2.1544-2.25250.32141490.26022581X-RAY DIFFRACTION99
2.2525-2.37120.29961370.25392578X-RAY DIFFRACTION99
2.3712-2.51980.27571290.25572619X-RAY DIFFRACTION99
2.5198-2.71430.29271330.25722593X-RAY DIFFRACTION99
2.7143-2.98730.29681230.26082640X-RAY DIFFRACTION100
2.9873-3.41940.25821330.24462616X-RAY DIFFRACTION100
3.4194-4.30730.24661240.21122661X-RAY DIFFRACTION100
4.3073-39.83860.25241720.21882663X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07880.3829-0.4413.2104-0.77774.083-0.1914-0.741-0.73660.1246-0.2283-0.02690.52330.13680.22250.15510.02390.05780.35560.1080.3002-19.98084.454333.6085
26.01742.4518-5.36653.6194-3.02565.58490.2495-0.20220.26990.29430.01330.1514-0.4441-0.1067-0.25570.1359-0.00250.01470.3447-0.01640.2384-21.909713.877831.8966
32.8456-0.7172-2.18333.21112.36536.2866-0.3326-0.5595-0.60.4219-0.2650.38860.64540.31830.61880.2195-0.03820.05360.4810.12320.3249-12.24116.561831.4401
40.113-0.1623-0.22921.43092.16874.6271-0.04750.05060.20050.55270.27060.0531-1.1029-0.785-0.29470.75090.270.1270.4723-0.11561.1033-3.869-12.671516.6515
58.0473-5.9528-1.50914.92231.23891.76630.09680.8703-0.1661-0.086-0.58970.26360.3853-0.35070.31970.32230.00140.01690.2614-0.02120.1957-3.6447-1.479212.2027
65.94323.53796.02443.41093.18998.8811-0.234-0.12130.49820.28040.18670.4015-0.32590.0972-0.07460.17760.08380.03580.3123-0.05180.2274-9.212914.804824.254
72.6131-1.835-0.30165.62593.16463.23590.0232-0.3203-0.15880.1343-0.0913-0.13520.157-0.0626-0.0040.1990.03240.00440.27870.10450.20712.432-0.732325.7021
84.8602-1.5729-0.59983.52640.16422.31590.1830.34860.0603-0.2053-0.29670.17620.1584-0.22640.0950.1136-0.010.00560.1419-0.01310.11250.67969.801813.2023
92.9176-0.0835-0.04642.6186-0.41142.8760.04880.22640.3671-0.33890.0887-0.1358-0.16410.0853-0.13090.2046-0.01690.02340.13180.01110.16388.17839.131716.2763
101.0364-1.2655-1.00882.77641.08621.682-0.0050.03050.10690.07950.0214-0.123-0.05240.0861-0.03320.11190.01110.00540.16390.00880.106812.318122.371416.4205
112.9359-0.4648-1.55171.42520.87155.07390.01490.0002-0.05380.0756-0.0676-0.09740.0525-0.01720.110.107-0.0056-0.00760.08670.01290.111612.456613.496816.9692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 12:27)
2X-RAY DIFFRACTION2(chain A and resid 28:52)
3X-RAY DIFFRACTION3(chain A and resid 53:78)
4X-RAY DIFFRACTION4(chain A and resid 79:87)
5X-RAY DIFFRACTION5(chain A and resid 88:106)
6X-RAY DIFFRACTION6(chain A and resid 107:124)
7X-RAY DIFFRACTION7(chain A and resid 125:154)
8X-RAY DIFFRACTION8(chain A and resid 155:194)
9X-RAY DIFFRACTION9(chain B and resid 12:79)
10X-RAY DIFFRACTION10(chain B and resid 86:140)
11X-RAY DIFFRACTION11(chain B and resid 141:195)

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