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- PDB-5cw8: Crystal structure of Mycobacterium tuberculosis KstR in complex w... -

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Basic information

Entry
Database: PDB / ID: 5cw8
TitleCrystal structure of Mycobacterium tuberculosis KstR in complex with 3-oxo-4-cholesten-26-oyl-CoA
ComponentsHTH-type transcriptional repressor KstR
KeywordsTranscription regulator / Transcriptional repressor / TetR family Transcriptional repressor / cholesterol 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
Chem-55X / TRIETHYLENE GLYCOL / HTH-type transcriptional repressor KstR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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) 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 27, 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 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)47,0245
Polymers44,7052
Non-polymers2,3183
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-13 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.694, 67.095, 124.231
Angle α, β, γ (deg.)90.00, 96.74, 90.00
Int Tables number5
Space group name H-MI121

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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-55X / S-{1-[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,7-dihydroxy-6,6-dimethyl-3-oxido-8,12 -dioxo-2,4-dioxa-9,13-diaza-3lambda~5~-phosphapentadecan-15-yl} (2S,6R)-6-[(8S,9S,10R,13R,14S,17R)-10,13-dimethyl-3-oxo-2,3,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta [a]phenanthren-17-yl]-2-methylheptanethioate (non-preferred name) / S-{1-[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxi do-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (2S,6R)-6-[(8S,9S,10R,13R,14R,17S)-10,13-dimethyl-3-oxo-2,3,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta [a]phenanthren-17-yl]-2-methylheptanethioate (non-preferred name)


Mass: 1084.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H75N7O15P2S
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.01 M nickel (II) chloride hexahydrate, 0.1 M Tris pH 8.5, 1.0 M lithium sulfate monohydrate

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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: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→47.8 Å / Num. obs: 12603 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 6.7
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BJB

3bjb


Resolution: 2.6→47.797 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 640 5.08 %Random selection
Rwork0.194 ---
obs0.1962 12598 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→47.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 69 66 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012952
X-RAY DIFFRACTIONf_angle_d0.6543731
X-RAY DIFFRACTIONf_dihedral_angle_d14.01964
X-RAY DIFFRACTIONf_chiral_restr0.03452
X-RAY DIFFRACTIONf_plane_restr0.003466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.80080.32341290.25682356X-RAY DIFFRACTION100
2.8008-3.08260.27881240.23862392X-RAY DIFFRACTION100
3.0826-3.52850.28511280.20832375X-RAY DIFFRACTION100
3.5285-4.44510.18791300.16852393X-RAY DIFFRACTION100
4.4451-47.80490.20211290.16782442X-RAY DIFFRACTION100

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