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

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Basic information

Entry
Database: PDB / ID: 5aqc
TitleKstR, transcriptional repressor of cholesterol degradation in Mycobacterium tuberculosis, bound to the cholesterol coenzyme A derivative, (25R)-3-oxocholest-4-en-26-oyl-CoA.
ComponentsHTH-TYPE TRANSCRIPTIONAL REPRESSOR KSTR
KeywordsTRANSCRIPTION
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
(25S)-3-oxocholest-4-en-26-oyl-CoA / HTH-type transcriptional repressor KstR
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsPodust, L.M. / Ouellet, H.
CitationJournal: To be Published
Title: Kstr, Transcriptional Repressor of Cholesterol Degradation in Mycobacterium Tuberculosis, Bound to the Cholesterol Coenzyme a Derivative, (25S)-3- Oxocholest-4-En-26-Oyl-Coa.
Authors: Podust, L.M. / Ouellet, H.
History
DepositionSep 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: HTH-TYPE TRANSCRIPTIONAL REPRESSOR KSTR
B: HTH-TYPE TRANSCRIPTIONAL REPRESSOR KSTR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4038
Polymers45,6502
Non-polymers2,7536
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-48.2 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.329, 67.404, 49.923
Angle α, β, γ (deg.)90.00, 105.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 233 molecules

#2: Chemical ChemComp-5JB / (25S)-3-oxocholest-4-en-26-oyl-CoA


Mass: 1164.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H76N7O18P3S
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details2-METHYL-2,4-PENTANEDIOL (MPD): PART OF CRYSTALLIZATION CONDITIONS SULFATE ION (SO4): PART OF ...2-METHYL-2,4-PENTANEDIOL (MPD): PART OF CRYSTALLIZATION CONDITIONS SULFATE ION (SO4): PART OF CRYSTALLIZATION CONDITIONS GLYCEROL (GOL): CRYOPROTECTANT (25S)-3-OXOCHOLEST-4-EN-26-OYL-COA (5JB): LIGAND OF THE KSTR TRANSCRIPTIONAL REPRESSOR. ONLY 3-OXOCHOLEST-4-EN-26-OYL END IS VISIBLE IN THE STRUCTURE
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: 2.15 Å3/Da / Density % sol: 42.8 % / Description: NONE
Crystal growpH: 7 / Details: 11% PEG 3350, 90 MM NASO4, 22% MPD, pH 7

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESERCH / Detector: CCD / Date: Sep 3, 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: 1.66→61.29 Å / Num. obs: 44460 / % possible obs: 92.4 % / Observed criterion σ(I): 1.2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.6
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.2 / % possible all: 62.2

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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: 1.66→61.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.616 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22604 2244 5.1 %RANDOM
Rwork0.1838 ---
obs0.18603 42163 92.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å2-0.08 Å2
2--0.23 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.66→61.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 93 227 3046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192932
X-RAY DIFFRACTIONr_bond_other_d0.0010.022869
X-RAY DIFFRACTIONr_angle_refined_deg1.941.993996
X-RAY DIFFRACTIONr_angle_other_deg0.93736535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9345379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35522.759116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7115468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.321528
X-RAY DIFFRACTIONr_chiral_restr0.1220.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023327
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02665
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_it2.5562.5431498
X-RAY DIFFRACTIONr_mcbond_other2.5382.5421497
X-RAY DIFFRACTIONr_mcangle_it3.4483.7931883
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3762.8521434
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: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 99 -
Rwork0.357 1893 -
obs--56.19 %

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