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- PDB-5ua1: Mycobacterium tuberculosis KstR in complex with a 18-bp DNA operator -

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Basic information

Entry
Database: PDB / ID: 5ua1
TitleMycobacterium tuberculosis KstR in complex with a 18-bp DNA operator
Components
  • DNA (5'-D(*AP*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*AP*T)-3')
  • DNA (5'-D(*AP*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*GP*T)-3')
  • HTH-type transcriptional repressor KstR
KeywordsTranscription/DNA / KstR / DNA / complex / transcriptional regulator / TetR family transcriptional repressor / Structural Genomics TB Structural Genomics Consortium / TBSGC / Transcription-DNA complex
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 / DNA / DNA (> 10) / HTH-type transcriptional repressor KstR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHo, N.A.T. / Dawes, S.S. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC)
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC)12/1111 New Zealand
CitationJournal: To Be Published
Title: Crystal structure of KstR in complex with cognate DNA operator
Authors: Ho, N.A.T. / Dawes, S.S. / Baker, E.N. / Lott, J.S.
History
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: HTH-type transcriptional repressor KstR
A: HTH-type transcriptional repressor KstR
C: DNA (5'-D(*AP*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*AP*T)-3')
D: DNA (5'-D(*AP*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*GP*T)-3')
E: DNA (5'-D(*AP*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*AP*T)-3')
F: DNA (5'-D(*AP*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,25610
Polymers66,7636
Non-polymers4924
Water724
1
B: HTH-type transcriptional repressor KstR
A: HTH-type transcriptional repressor KstR
C: DNA (5'-D(*AP*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*AP*T)-3')
D: DNA (5'-D(*AP*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2278
Polymers55,7344
Non-polymers4924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HTH-type transcriptional repressor KstR
A: HTH-type transcriptional repressor KstR
E: DNA (5'-D(*AP*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*AP*T)-3')
F: DNA (5'-D(*AP*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2278
Polymers55,7344
Non-polymers4924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.423, 79.280, 116.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#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 (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: kstR, Rv3574 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96856

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA (5'-D(*AP*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*AP*T)-3')


Mass: 5514.603 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
#3: DNA chain DNA (5'-D(*AP*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*GP*T)-3')


Mass: 5514.603 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)

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Non-polymers , 3 types, 8 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 15% PEG 3350, 9% MPD, 0.2 M Li2SO4, 0.1 M imidazole-HCl

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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: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→48.56 Å / Num. obs: 24284 / % possible obs: 100 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.155 / Net I/σ(I): 9.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.47 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CXG

5cxg


Resolution: 2.9→46.853 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 1233 5.09 %Random selection
Rwork0.2293 ---
obs0.2312 24235 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→46.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 1464 18 4 4047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034248
X-RAY DIFFRACTIONf_angle_d0.5196058
X-RAY DIFFRACTIONf_dihedral_angle_d22.8582278
X-RAY DIFFRACTIONf_chiral_restr0.03709
X-RAY DIFFRACTIONf_plane_restr0.003521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.01610.42691180.34252564X-RAY DIFFRACTION100
3.0161-3.15340.34851590.31892537X-RAY DIFFRACTION100
3.1534-3.31960.33681400.28442553X-RAY DIFFRACTION99
3.3196-3.52750.3021450.23852547X-RAY DIFFRACTION100
3.5275-3.79970.23981260.23022571X-RAY DIFFRACTION100
3.7997-4.18190.25991320.20162570X-RAY DIFFRACTION100
4.1819-4.78650.20711270.19482567X-RAY DIFFRACTION100
4.7865-6.02850.2621500.21472546X-RAY DIFFRACTION100
6.0285-46.85910.22931360.19372547X-RAY DIFFRACTION99

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