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- PDB-5mwo: Structure of Mycobacterium Tuberculosis Transcriptional Regulator... -

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Basic information

Entry
Database: PDB / ID: 5mwo
TitleStructure of Mycobacterium Tuberculosis Transcriptional Regulatory Repressor Protein (EthR) in complex with fragment 7E8.
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / EthR / Repressor / TetR / 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 / 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 / Homeobox-like domain superfamily ...: / 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
(5-methyl-1-benzothiophen-2-yl)methanol / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.962 Å
AuthorsMendes, V. / Chan, D.S.-H. / Thomas, S.E. / McConnell, B. / Matak-Vinkovic, D. / Coyne, A.G. / Abell, C. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Fragment Screening against the EthR-DNA Interaction by Native Mass Spectrometry.
Authors: Chan, D.S. / Mendes, V. / Thomas, S.E. / McConnell, B.N. / Matak-Vinkovic, D. / Coyne, A.G. / Blundell, T.L. / Abell, C.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 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)25,6784
Polymers25,2591
Non-polymers4193
Water1,36976
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3568
Polymers50,5192
Non-polymers8376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2940 Å2
ΔGint-19 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.927, 121.927, 33.728
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-409-

HOH

21A-471-

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 H37Rv (bacteria)
Gene: ethR, etaR, Rv3855 / Production host: Escherichia coli (E. coli) / Variant (production host): DH5a / References: UniProt: P9WMC1
#2: Chemical ChemComp-J6W / (5-methyl-1-benzothiophen-2-yl)methanol


Mass: 178.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10OS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 50.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.7 to 2.1 M ammonium sulfate 0.1 M MES (pH 6 to 7) 5 to 15%(v/v) glycerol 7 to 12%(v/v) 1,4-dioxane
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.96→121.93 Å / Num. obs: 18535 / % possible obs: 98.2 % / Redundancy: 12.8 % / Biso Wilson estimate: 27.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.056 / Rrim(I) all: 0.202 / Net I/σ(I): 11.9 / Num. measured all: 236428 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
1.96-2.0712.91.4790.3890.4241.539
6.2-121.93110.040.9990.0120.042

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.962→86.215 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.74
RfactorNum. reflection% reflection
Rfree0.2589 888 4.8 %
Rwork0.1983 --
obs0.2012 18489 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.77 Å2 / Biso mean: 40.3552 Å2 / Biso min: 13.5 Å2
Refinement stepCycle: final / Resolution: 1.962→86.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 28 76 1591
Biso mean--65.68 42.89 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071547
X-RAY DIFFRACTIONf_angle_d0.8352110
X-RAY DIFFRACTIONf_chiral_restr0.045241
X-RAY DIFFRACTIONf_plane_restr0.006272
X-RAY DIFFRACTIONf_dihedral_angle_d16.778906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.962-2.0850.38461380.337529223060100
2.085-2.2460.35751480.269929103058100
2.246-2.4720.24191360.220127832919100
2.472-2.82970.23671550.191629753130100
2.8297-3.56520.25761610.186329833144100
3.5652-86.29870.22571500.16033028317895
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.4826-3.2438-2.51527.18243.11673.01040.23870.6426-0.0068-1.19540.045-0.3777-0.7315-0.0746-0.22020.5692-0.1120.04020.24680.00960.35324.762851.0835-6.3602
23.39011.24330.91719.3559-1.04214.2292-0.06750.159-0.3381-0.38040.4087-0.63420.28550.0016-0.35410.5671-0.1863-0.08410.2692-0.02180.413928.467859.282-1.1973
35.725.408-1.91064.9616-1.90772.65090.42870.04890.5340.6588-0.22120.2843-0.9309-0.2919-0.19220.48610.07010.00190.2818-0.03890.293414.844141.91683.3254
44.61620.0457-0.10947.179-1.77525.74490.08430.1841-0.0690.02550.28231.31430.0348-0.7823-0.350.25380.064-0.06710.29390.01230.38355.077528.0067-1.9323
54.82830.17965.00834.5780.64695.41240.45120.2731-0.3389-0.55750.0401-0.54430.30750.4428-0.4130.3472-0.01170.01770.19190.01690.342325.424838.4576-2.032
64.70364.7315-0.17539.0672-0.81042.9693-0.0902-0.39240.22910.28810.0510.3259-0.422-0.34110.0410.26110.1176-0.02030.2870.00090.151312.76525.962710.3049
72.9969-0.208-0.53643.558-1.21895.1149-0.16670.07320.0342-0.14880.0556-0.1520.0307-0.1460.09730.12970.0506-0.0150.1275-0.00580.193316.580822.5329-2.673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 46 )A22 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 67 )A47 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 92 )A68 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 115 )A93 - 115
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 131 )A116 - 131
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 167 )A132 - 167
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 214 )A168 - 214

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