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- PDB-5fmp: KstR, transcriptional repressor of cholesterol degradation in Myc... -

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Basic information

Entry
Database: PDB / ID: 5fmp
TitleKstR, transcriptional repressor of cholesterol degradation in Mycobacterium tuberculosis, bound to the DNA operator
Components
  • 5'-D(*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*A)-3'
  • 5'-D(*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*G)-3'
  • HTH-TYPE TRANSCRIPTIONAL REPRESSOR KSTR
KeywordsDNA BINDING PROTEIN
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
DNA / DNA (> 10) / HTH-type transcriptional repressor KstR
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsPodust, L.M. / Ouellet, H.
CitationJournal: To be Published
Title: Kstr, Transcriptional Repressor of Cholesterol Degradation in Mycobacterium Tuberculosis
Authors: Podust, L.M. / Ouellet, H.
History
DepositionNov 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
C: 5'-D(*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*A)-3'
D: 5'-D(*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)55,4444
Polymers55,4444
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-38.5 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.530, 62.781, 98.647
Angle α, β, γ (deg.)90.00, 89.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HTH-TYPE TRANSCRIPTIONAL REPRESSOR KSTR / KSTR


Mass: 22825.016 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 23-220
Source method: isolated from a genetically manipulated source
Details: ENGINEERED 6-HIS TAG AT THE C-TERMINUS / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96856
#2: DNA chain 5'-D(*CP*TP*AP*GP*AP*AP*CP*GP*TP*GP*TP*TP*CP*TP*AP*A)-3'


Mass: 4897.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) MYCOBACTERIUM TUBERCULOSIS (bacteria)
#3: DNA chain 5'-D(*TP*TP*AP*GP*AP*AP*CP*AP*CP*GP*TP*TP*CP*TP*AP*G)-3'


Mass: 4897.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) MYCOBACTERIUM TUBERCULOSIS (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Sequence details22 AMINO ACID RESIDUES AT THE N-TERMINUS ARE TRUNCATED. 6- HIS TAG IS ENGINEERED AT THE C-TERMINUS

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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: 2.4 Å3/Da / Density % sol: 48.5 % / Description: NONE
Crystal growpH: 5.1
Details: 0.2 M SODIUM SULFATE, 8% TACSIMATE, PH 5.1; 21.7% PEG 6000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 23, 2015 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.26→49.51 Å / Num. obs: 20253 / % possible obs: 87.3 % / Observed criterion σ(I): 0.5 / Redundancy: 2.4 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.7 / % possible all: 50.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MNL

3mnl


Resolution: 2.26→44.31 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.928 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27039 1036 5.1 %RANDOM
Rwork0.20182 ---
obs0.20539 19214 87.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.149 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å20 Å20.56 Å2
2--3.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.26→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 650 0 96 3543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0183587
X-RAY DIFFRACTIONr_bond_other_d0.0010.023150
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.7794990
X-RAY DIFFRACTIONr_angle_other_deg0.96437182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1915369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.70721.52125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03715480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5851538
X-RAY DIFFRACTIONr_chiral_restr0.0730.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2183.3421476
X-RAY DIFFRACTIONr_mcbond_other2.2163.3411475
X-RAY DIFFRACTIONr_mcangle_it3.4835.0031845
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6513.3182111
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 36 -
Rwork0.321 733 -
obs--44.25 %

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