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- PDB-3mnl: The crystal structure of KstR (Rv3574) from Mycobacterium tubercu... -

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Basic information

Entry
Database: PDB / ID: 3mnl
TitleThe crystal structure of KstR (Rv3574) from Mycobacterium tuberculosis H37Rv
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY)
KeywordsTRANSCRIPTION REGULATOR / tetR family of transcriptional regulator / all-helical / DNA-binding / hydrophobic ligand-binding / 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
TRIETHYLENE GLYCOL / HTH-type transcriptional repressor KstR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGao, C. / Bunker, R.D. / ten Bokum, A. / Kendall, S.L. / Stoker, N.G. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC)
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
DepositionApr 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY)
B: TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9235
Polymers44,4732
Non-polymers4513
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-18 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.020, 54.570, 165.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) / KstR


Mass: 22236.330 Da / Num. of mol.: 2 / Mutation: M1V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3574 / Plasmid: pDEST-566 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96856
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17.5% PEG 3350, 0.2M ammonium fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953692 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953692 Å / Relative weight: 1
ReflectionResolution: 1.8→165.99 Å / Num. obs: 35558 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.25 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5095 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
BUSTER2.9.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BJB

3bjb


Resolution: 1.8→24.79 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1813 5.11 %RANDOM
Rwork0.1909 ---
obs0.192 35467 --
Displacement parametersBiso max: 95.01 Å2 / Biso mean: 31.05 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.9534 Å20 Å20 Å2
2---2.1821 Å20 Å2
3---1.2287 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 19 117 2894
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092823HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.853816HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d978SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes429HARMONIC5
X-RAY DIFFRACTIONt_it2823HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion15.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion384SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3440SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2359 144 5.04 %
Rwork0.204 2711 -
all0.206 2855 -
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)
13.9990.48272.0561.50130.68265.3752-0.041-0.16290.291-0.03680.1324-0.0998-0.47270.2255-0.0913-0.0636-0.06430.0513-0.0101-0.11380.008816.894313.550235.481
22.54151.0950.45055.20861.15185.59870.0533-0.3170.30870.00350.0584-0.2697-0.19330.5283-0.1116-0.172-0.01990.00420.0081-0.1068-0.052616.95048.174234.347
30.71092.91040.32073.5884-1.704100.0520.04070.09010.27180.30290.2425-0.0903-0.2454-0.355-0.03030.02660.09560.09240.06070.0243-3.2729-7.961237.1116
46.4588-1.29171.50092.756-0.16923.7497-0.0220.21750.0761-0.15770.01660.0787-0.24390.09990.0054-0.0623-0.04430.0105-0.0459-0.02-0.05158.42736.422925.2606
51.28640.2116-1.98012.2729-1.61261.85870.10550.0288-0.1994-0.07820.0843-0.53270.19830.3161-0.1898-0.0658-0.0108-0.01990.0545-0.0360.0816.1983-3.611529.7215
63.2157-2.84961.72195.1873-2.68023.49620.0465-0.1626-0.09730.0740.0130.12250.0328-0.1148-0.0594-0.0869-0.0344-0.00880.0011-0.0336-0.03952.4861-7.938227.3225
72.20710.93350.35970.03861.2392.0978-0.0002-0.20920.05580.0114-0.05880.27070.2038-0.24550.059-0.0279-0.1195-0.01230.1004-0.00070.0012-5.2894-15.43626.2054
80.18120.99270.59940-0.38160.05330.00280.01050.0019-0.0369-0.01480.13770.0015-0.00740.0120.16060.04390.0001-0.04020.024-0.10321.38813.7815-12.0686
91.2751-0.2177-0.86082.958-0.68712.26410.18370.25520.175-0.2614-0.087-0.0879-0.5442-0.2256-0.09670.16840.080.0878-0.10790.0242-0.14478.44855.9717-1.7375
1000.3819-0.57160.29630.48820.7670.0184-0.023-0.068400.0011-0.01270.0142-0.0463-0.01950.12790.06660.07130.0509-0.10150.02665.5781-25.2815-0.1442
117.92342.1644-2.91040.007-0.4282.02190.05840.2509-0.31130.13890.16880.05010.11590.1465-0.22720.02580.0709-0.0666-0.0614-0.0412-0.06019.3022-19.86728.1316
125.4062-2.282-0.48316.07091.45496.16510.0028-0.47220.1065-0.3680.14510.161-0.5155-0.1908-0.14790.06460.00570.0099-0.14360.0139-0.15988.54560.91318.5033
132.40311.12691.88382.19591.46942.2398-0.0960.1984-0.0004-0.17670.01380.0095-0.0337-0.04390.08220.0251-0.0057-0.0140.0177-0.0278-0.05252.4529-12.47311.2987
142.56080.638-2.04654.0718-1.57693.9060.1128-0.159-0.1591-0.1724-0.1048-0.19610.5050.3169-0.00810.04340.0652-0.0585-0.0548-0.0269-0.024112.7852-16.735318.504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|9 - A|44 }A9 - 44
2X-RAY DIFFRACTION2{ A|45 - A|78 }A45 - 78
3X-RAY DIFFRACTION3{ A|79 - A|105 }A79 - 105
4X-RAY DIFFRACTION4{ A|106 - A|122 }A106 - 122
5X-RAY DIFFRACTION5{ A|123 - A|136 }A123 - 136
6X-RAY DIFFRACTION6{ A|137 - A|183 }A137 - 183
7X-RAY DIFFRACTION7{ A|184 - A|197 }A184 - 197
8X-RAY DIFFRACTION8{ B|11 - B|18 }B11 - 18
9X-RAY DIFFRACTION9{ B|19 - B|77 }B19 - 77
10X-RAY DIFFRACTION10{ B|78 - B|86 }B78 - 86
11X-RAY DIFFRACTION11{ B|87 - B|104 }B87 - 104
12X-RAY DIFFRACTION12{ B|105 - B|130 }B105 - 130
13X-RAY DIFFRACTION13{ B|131 - B|173 }B131 - 173
14X-RAY DIFFRACTION14{ B|174 - B|194 }B174 - 194

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