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- PDB-5f1j: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -

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Basic information

Entry
Database: PDB / ID: 5f1j
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 1 at 1.63A resolution
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / EthR / repressor / Mycobacterium tuberculosis
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
: / Transcriptional regulator EthR, C-terminal domain / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like ...: / Transcriptional regulator EthR, C-terminal domain / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-cyclopentyl-1-pyrrolidin-1-yl-propan-1-one / HTH-type transcriptional regulator EthR / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.631 Å
AuthorsSurade, S. / Blaszczyk, M. / Nikiforov, P.O. / Abell, C. / Blundell, T.L.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Bill & Melinda Gates Foundation United States
European Union
CitationJournal: Org.Biomol.Chem. / Year: 2016
Title: A fragment merging approach towards the development of small molecule inhibitors of Mycobacterium tuberculosis EthR for use as ethionamide boosters.
Authors: Nikiforov, P.O. / Surade, S. / Blaszczyk, M. / Delorme, V. / Brodin, P. / Baulard, A.R. / Blundell, T.L. / Abell, C.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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
A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6503
Polymers25,2591
Non-polymers3912
Water2,936163
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3006
Polymers50,5192
Non-polymers7814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3070 Å2
ΔGint-22 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.810, 121.810, 33.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

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Components

#1: Protein HTH-type transcriptional regulator EthR


Mass: 25259.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Gene: ethR, etaR, MT3970 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMC0, UniProt: P9WMC1*PLUS
#2: Chemical ChemComp-5TO / 3-cyclopentyl-1-pyrrolidin-1-yl-propan-1-one


Mass: 195.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium sulphate, Glycerol, MES / PH range: 6.3 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.631→43.066 Å / Num. all: 32327 / Num. obs: 32327 / % possible obs: 99.8 % / Redundancy: 13.1 % / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Rsym value: 0.065 / Net I/av σ(I): 8.05 / Net I/σ(I): 23 / Num. measured all: 424257
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.63-1.678.90.71.12091223520.2590.72.999.8
1.67-1.7211.60.6351.22636822710.2010.6353.899.4
1.72-1.7713.30.5091.52983022370.1490.5095.299.7
1.77-1.8213.50.4071.92888521350.1180.4076.699.9
1.82-1.8813.60.2882.72889921250.0840.2889.299.8
1.88-1.9513.80.2473.12776320100.0710.2471199.9
1.95-2.0213.80.1764.32712919650.0510.17614.999.9
2.02-2.11140.1375.52693819260.0390.13719.199.8
2.11-2.214.10.1126.62528317990.0320.11222.799.8
2.2-2.3114.10.0928.12456917460.0260.09227.199.8
2.31-2.4314.10.0779.52370116860.0220.07731.499.9
2.43-2.58140.066112214515790.0190.06635.599.9
2.58-2.7613.90.0611.62054014810.0170.0638.3100
2.76-2.9813.60.05512.51912714070.0160.05541.5100
2.98-3.2613.10.047141686112870.0140.04744.4100
3.26-3.6512.90.041151533511910.0120.04149.6100
3.65-4.21130.03915.51387410650.0110.03953.199.8
4.21-5.1613.10.03416.6117548940.010.0345599.9
5.16-7.2913.20.03615.595947270.0110.03652.8100
7.29-43.06610.70.03614.947504440.0120.03649.298.6

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.631→33.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2223 / WRfactor Rwork: 0.1945 / FOM work R set: 0.8799 / SU B: 1.543 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0872 / SU Rfree: 0.0892 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1634 5.1 %RANDOM
Rwork0.1966 ---
obs0.1982 30596 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 342.05 Å2 / Biso mean: 25.59 Å2 / Biso min: 7.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.631→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 28 163 1701
Biso mean--22.51 46.54 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221571
X-RAY DIFFRACTIONr_angle_refined_deg2.2731.9612139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22823.78474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6915242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3691513
X-RAY DIFFRACTIONr_chiral_restr0.1640.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211198
X-RAY DIFFRACTIONr_mcbond_it1.5711.5968
X-RAY DIFFRACTIONr_mcangle_it2.67721554
X-RAY DIFFRACTIONr_scbond_it4.0443603
X-RAY DIFFRACTIONr_scangle_it6.4344.5585
LS refinement shellResolution: 1.631→1.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 112 -
Rwork0.333 2198 -
all-2310 -
obs--100 %

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