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

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Basic information

Entry
Database: PDB / ID: 5mys
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound GSK920684A at 1.59A resolution
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / EthR / Mycobacterium tuberculosis / represor
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 ...: / 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
Chem-YP6 / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.587 Å
AuthorsBlaszczyk, M. / Mendes, V. / Mugumbate, G. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Front Pharmacol / Year: 2017
Title: Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach.
Authors: Mugumbate, G. / Mendes, V. / Blaszczyk, M. / Sabbah, M. / Papadatos, G. / Lelievre, J. / Ballell, L. / Barros, D. / Abell, C. / Blundell, T.L. / Overington, J.P.
History
DepositionJan 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _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)25,5892
Polymers25,2591
Non-polymers3291
Water1,838102
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1774
Polymers50,5192
Non-polymers6592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2730 Å2
ΔGint-22 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.549, 121.549, 33.790
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-439-

HOH

21A-498-

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 (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ethR, etaR, Rv3855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WMC1
#2: Chemical ChemComp-YP6 / 2-(3-fluoranylphenoxy)-~{N}-(4-pyridin-2-yl-1,3-thiazol-2-yl)ethanamide


Mass: 329.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12FN3O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.7 to 2.1 ammonium sulfate 0.1M MES (pH 6 to 7) 5 to 15%(v/v) glycerol 7 to 12%(v/v) 1,4-dioxane
PH range: 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 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.587→121.549 Å / Num. all: 34673 / Num. obs: 34673 / % possible obs: 99.2 % / Redundancy: 12.4 % / Biso Wilson estimate: 24.8 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.066 / Rsym value: 0.061 / Net I/av σ(I): 7 / Net I/σ(I): 22 / Num. measured all: 431353
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.59-1.6710.71.1410.70.3741.2491.14196.5
1.67-1.77130.77610.2290.8350.77698.8
1.77-1.913.10.4441.60.130.4760.44499.4
1.9-2.05130.2293.10.0670.2450.22999.7
2.05-2.2412.90.1255.80.0370.1340.12599.8
2.24-2.5112.90.0890.0240.0850.0899.9
2.51-2.912.70.05712.10.0170.0610.05799.9
2.9-3.5512.40.04314.20.0130.0460.043100
3.55-5.0211.60.03815.60.0120.0410.03899.9
5.02-121.54910.70.03415.30.0110.0370.03499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å85.95 Å
Translation2.5 Å85.95 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.587→85.948 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.94
RfactorNum. reflection% reflection
Rfree0.2081 1743 5.04 %
Rwork0.1729 --
obs0.1746 34616 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.71 Å2 / Biso mean: 38.3378 Å2 / Biso min: 15.33 Å2
Refinement stepCycle: final / Resolution: 1.587→85.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 23 102 1620
Biso mean--75.01 45.69 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061558
X-RAY DIFFRACTIONf_angle_d0.7722126
X-RAY DIFFRACTIONf_chiral_restr0.047242
X-RAY DIFFRACTIONf_plane_restr0.005278
X-RAY DIFFRACTIONf_dihedral_angle_d14.949920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5867-1.63340.29671270.24922637276497
1.6334-1.68610.29741420.23262613275595
1.6861-1.74640.24771510.20182661281299
1.7464-1.81630.19681410.18852695283699
1.8163-1.8990.21011550.17612709286499
1.899-1.99910.20041490.17162732288199
1.9991-2.12440.18381520.158927152867100
2.1244-2.28840.17881320.151527552887100
2.2884-2.51870.18691350.160527672902100
2.5187-2.88320.18821590.173127822941100
2.8832-3.63260.20651580.172628062964100
3.6326-86.07440.22731420.17330013143100
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)
17.08330.11030.7215.4821-0.53814.0723-0.0578-0.66220.55340.1492-0.00330.0598-0.4584-0.5730.16610.2629-0.07630.00970.5421-0.04610.3316-53.3154-20.84024.8749
24.6784.00794.6965.24832.91387.40640.4545-0.8765-1.29320.7080.52720.09780.5021-0.0968-0.55970.3998-0.1282-0.07170.54170.19440.61-46.7068-32.12618.6348
35.42680.96690.34611.54130.83084.03860.2818-0.3482-0.42730.0056-0.0491-0.14310.02220.5192-0.18330.2644-0.1844-0.01190.5462-0.05620.3692-58.824-28.53571.1418
48.00485.5207-1.98953.8775-0.56613.227-0.14790.5740.1472-0.16590.3020.3447-0.1114-0.9668-0.13290.17820.0491-0.02680.437-0.01010.2283-41.5331-14.4598-3.481
53.90381.42591.26450.57020.59030.7830.213-0.03850.64770.08760.1025-0.0429-0.8984-0.2843-0.28670.90120.07720.2160.4641-0.18011.2794-26.78334.0181-0.2963
67.18392.0215-2.28494.5967-0.8744.79630.2403-0.01830.7187-0.0601-0.0481-0.0215-0.3773-0.048-0.10680.2490.0770.01910.2181-0.01510.2493-27.9804-7.57432.7046
73.53030.23340.13372.95953.74364.62140.0391-0.0592-0.77480.0970.3228-0.60440.7079-0.1128-0.38480.3006-0.05550.00840.4399-0.01260.4743-38.0736-25.28732.0589
87.2794.1499-0.6155.5849-0.37813.3915-0.12270.35950.0415-0.43660.02380.0742-0.1152-0.51720.07850.22740.0857-0.00990.2802-0.01490.17-29.3822-14.3841-10.0096
90.64421.10250.12142.0960.8413.97430.31810.02560.3133-0.0359-0.28410.0901-0.51050.57530.01210.3254-0.04350.07660.28850.0370.3287-13.2183-5.8877-11.1611
101.91970.2721-1.63962.1825-2.24676.6210.04060.03-0.0097-0.01880.10370.1180.02-0.2594-0.14190.17710.0217-0.00590.1929-0.00520.2014-24.9066-18.9216-1.1487
113.62710.6673-2.50974.48234.06376.4589-0.2847-0.2663-0.85240.29350.1275-0.57710.8399-0.14260.20110.28560.01930.0360.23310.04710.2703-24.8888-24.629312.1752
121.94291.3672-1.45093.0777-2.40146.64530.0977-0.18330.16340.1575-0.00360.037-0.33510.0624-0.12710.21610.0332-0.00120.1605-0.02680.2205-19.0139-10.95923.8918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 38 )A22 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 46 )A39 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 67 )A47 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 92 )A68 - 92
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 98 )A93 - 98
6X-RAY DIFFRACTION6chain 'A' and (resid 99 through 115 )A99 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 131 )A116 - 131
8X-RAY DIFFRACTION8chain 'A' and (resid 132 through 158 )A132 - 158
9X-RAY DIFFRACTION9chain 'A' and (resid 159 through 167 )A159 - 167
10X-RAY DIFFRACTION10chain 'A' and (resid 168 through 188 )A168 - 188
11X-RAY DIFFRACTION11chain 'A' and (resid 189 through 195 )A189 - 195
12X-RAY DIFFRACTION12chain 'A' and (resid 196 through 214 )A196 - 214

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