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

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Basic information

Entry
Database: PDB / ID: 5mym
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound GSK2032710A at 2.28A 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 / 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
Chem-HYV / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsMendes, V. / Blaszczyk, M. / 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 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator EthR
B: HTH-type transcriptional regulator EthR
C: HTH-type transcriptional regulator EthR
D: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,15610
Polymers101,0374
Non-polymers1,1196
Water4,576254
1
A: HTH-type transcriptional regulator EthR
B: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0785
Polymers50,5192
Non-polymers5603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-16 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: HTH-type transcriptional regulator EthR
D: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0785
Polymers50,5192
Non-polymers5603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-16 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.622, 56.481, 98.188
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 17 and (name O or name...
21(chain D and ((resid 17 and (name N or name...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHR(chain A and ((resid 17 and (name O or name...AA1721
12GLUGLU(chain A and ((resid 17 and (name O or name...AA17 - 21421 - 218
13GLUGLU(chain A and ((resid 17 and (name O or name...AA17 - 21421 - 218
14GLUGLU(chain A and ((resid 17 and (name O or name...AA17 - 21421 - 218
15GLUGLU(chain A and ((resid 17 and (name O or name...AA17 - 21421 - 218
16GLUGLU(chain A and ((resid 17 and (name O or name...AA17 - 21421 - 218
21THRTHR(chain D and ((resid 17 and (name N or name...DD1721
22GLUGLU(chain D and ((resid 17 and (name N or name...DD17 - 21421 - 218
23GLUGLU(chain D and ((resid 17 and (name N or name...DD17 - 21421 - 218
24GLUGLU(chain D and ((resid 17 and (name N or name...DD17 - 21421 - 218
25GLUGLU(chain D and ((resid 17 and (name N or name...DD17 - 21421 - 218
26GLUGLU(chain D and ((resid 17 and (name N or name...DD17 - 21421 - 218

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Components

#1: Protein
HTH-type transcriptional regulator EthR


Mass: 25259.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ethR, etaR, Rv3855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WMC1
#2: Chemical ChemComp-HYV / [4-(phenylmethyl)piperidin-1-yl]-[1-(5-pyrrol-1-yl-1,3,4-thiadiazol-2-yl)piperidin-4-yl]methanone


Mass: 435.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H29N5OS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.02M Sodium/potassium phosphate 20% w/v PEG 3350

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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: 2.28→98.19 Å / Num. obs: 43150 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Net I/σ(I): 12.1 / Num. measured all: 146825 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.28-2.43.40.5510.7560.3520.65698.5
7.2-98.193.20.0240.9990.0160.02997.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.28 Å98.19 Å
Translation2.28 Å98.19 Å

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Processing

Software
NameVersionClassification
SCALA0.5.15data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 2.28→98.188 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.2
RfactorNum. reflection% reflection
Rfree0.2271 2173 5.04 %
Rwork0.1749 --
obs0.1776 43140 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.93 Å2 / Biso mean: 46.5863 Å2 / Biso min: 21.07 Å2
Refinement stepCycle: final / Resolution: 2.28→98.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6117 0 78 254 6449
Biso mean--67.07 47.89 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086326
X-RAY DIFFRACTIONf_angle_d0.9858624
X-RAY DIFFRACTIONf_chiral_restr0.051993
X-RAY DIFFRACTIONf_plane_restr0.0071122
X-RAY DIFFRACTIONf_dihedral_angle_d19.453766
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1798X-RAY DIFFRACTION8.431TORSIONAL
12D1798X-RAY DIFFRACTION8.431TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2776-2.32710.31161470.23962510265799
2.3271-2.38130.27651120.22662583269598
2.3813-2.44080.277990.21182541264098
2.4408-2.50680.23871560.20042508266498
2.5068-2.58060.27321440.20042574271898
2.5806-2.66390.27561220.19432518264098
2.6639-2.75910.2431450.18492541268699
2.7591-2.86960.26411550.19482508266398
2.8696-3.00020.32151460.19722572271899
3.0002-3.15840.22671330.19692566269999
3.1584-3.35630.24981340.19032566270099
3.3563-3.61540.2231480.16782537268598
3.6154-3.97930.20911160.16242620273698
3.9793-4.55510.18531520.142578273099
4.5551-5.73890.21651310.15692607273898
5.7389-98.27930.18081330.16192638277197
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)
11.6947-1.0553-2.00166.0317-0.99227.7597-0.0153-0.47250.2418-0.06740.19420.0388-0.2031-0.0991-0.23710.26670.0147-0.07520.3029-0.03380.3513.1416-46.109134.9542
24.87943.59492.28236.55152.23322.65790.10870.29870.1007-0.0221-0.16050.17240.0116-0.29890.06590.24610.01980.01220.2640.0810.261911.9463-40.593931.2744
35.54251.389-0.85364.13290.91544.1710.2453-0.9483-0.16411.0612-0.4481-0.24970.42610.15640.17610.58610.00670.00920.42730.11290.306624.513-25.143147.8062
45.9203-3.24665.06696.2328-3.37144.349-0.27050.44150.0524-0.0799-0.3091-0.2068-0.42180.29570.61510.4024-0.06040.01970.35170.03380.297818.8721-31.470128.0468
52.2471.12992.00445.04423.76457.13410.2688-0.45850.12070.622-0.4990.46180.4954-0.81070.13280.320.01440.04090.3110.02090.34915.368-15.561442.537
64.5443-1.0694-0.92675.20081.5575.08070.0319-0.1986-0.23270.1917-0.0509-0.28950.41490.1015-0.03450.296-0.02130.00760.25770.03520.266628.2273-19.123538.4929
71.7991-1.6316-0.47535.06851.03148.62470.14980.0973-0.1281-0.1948-0.20880.064-0.0684-0.8340.14350.2788-0.012-0.03870.3942-0.02630.262622.6772-12.4591-1.1004
88.81295.36786.71245.67626.82978.8055-0.14280.55020.1045-0.34780.1821-0.14460.06060.5853-0.00790.4008-0.02330.05590.33910.07870.266532.7681-10.377913.4718
93.4994-1.4213-0.11323.1938-1.6096.52820.091-0.28870.75340.4029-0.1631-0.2272-1.07190.3620.11330.4629-0.05010.07890.24860.00020.420733.6074-1.300628.6814
106.49221.37833.90042.60661.70078.51120.24860.0955-0.5485-0.13050.1303-0.28770.43560.2169-0.40740.28080.0320.07810.24650.00680.276132.995-15.580322.4979
114.3866-0.79140.97082.8532-0.13035.0694-0.0847-0.26840.1140.02480.1286-0.0025-0.0430.0299-0.05120.2662-0.02650.03860.25550.00980.247129.3505-10.591934.6218
12-0.001-0.00950.0165-0.03020.01060.0146-0.1079-2.00380.11970.72090.1261-0.5370.3278-0.5552-0.20040.50720.1128-0.04830.89670.26041.27755.8902-53.946856.4763
132.74510.41591.48685.528-0.49433.65140.1186-0.10560.24550.3067-0.24280.24890.1576-0.80710.13820.32720.02830.04380.4927-0.02610.289-22.2544-47.092149.6427
144.1924-4.7067-6.11726.50776.24789.39810.0475-0.5913-0.2480.0967-0.03080.0601-0.2990.5513-0.01980.40860.016-0.03520.410.04110.3411-10.573-49.596335.6111
153.841.14713.57022.798-0.95085.98980.29280.3609-0.8846-0.5449-0.1794-0.36861.20950.5999-0.19670.49510.0911-0.03610.25280.01040.4903-9.6955-58.765320.4497
165.9719-1.1356-3.60352.52091.32328.72670.2038-0.14280.48270.11970.1234-0.3043-0.38770.2485-0.37310.2628-0.0095-0.08210.22260.01390.298-10.3343-44.392626.5676
174.38041.0133-1.24113.1005-0.28555.6059-0.0490.2814-0.0869-0.00370.1115-0.06920.05240.0763-0.06190.22390.0266-0.04810.2361-0.00620.2254-13.9589-49.390214.4683
184.7917-1.2576-0.68515.0407-0.53943.80750.0274-0.23920.1660.21780.2041-0.22030.0233-0.2069-0.26250.3185-0.01230.03210.3292-0.04930.3684-31.3268-13.109120.3382
191.4012-1.3404-0.59795.66641.82120.85290.00610.2157-0.024-0.3713-0.18270.3542-0.0663-0.17660.20560.3526-0.0199-0.050.36970.04790.3155-25.9468-35.69658.0332
204.45780.79240.75524.63951.17264.86570.03680.20980.4446-0.0714-0.0795-0.1954-0.26240.15150.02090.29510.0166-0.00070.26760.02750.28-15.0779-40.690210.7027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 38 )A17 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 92 )A39 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 116 )A93 - 116
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 131 )A117 - 131
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 167 )A132 - 167
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 214 )A168 - 214
7X-RAY DIFFRACTION7chain 'B' and (resid 15 through 67 )B15 - 67
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 92 )B68 - 92
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 115 )B93 - 115
10X-RAY DIFFRACTION10chain 'B' and (resid 116 through 158 )B116 - 158
11X-RAY DIFFRACTION11chain 'B' and (resid 159 through 214 )B159 - 214
12X-RAY DIFFRACTION12chain 'C' and (resid 10 through 19 )C10 - 19
13X-RAY DIFFRACTION13chain 'C' and (resid 20 through 67 )C20 - 67
14X-RAY DIFFRACTION14chain 'C' and (resid 68 through 92 )C68 - 92
15X-RAY DIFFRACTION15chain 'C' and (resid 93 through 115 )C93 - 115
16X-RAY DIFFRACTION16chain 'C' and (resid 116 through 158 )C116 - 158
17X-RAY DIFFRACTION17chain 'C' and (resid 159 through 214 )C159 - 214
18X-RAY DIFFRACTION18chain 'D' and (resid 17 through 67 )D17 - 67
19X-RAY DIFFRACTION19chain 'D' and (resid 68 through 167 )D68 - 167
20X-RAY DIFFRACTION20chain 'D' and (resid 168 through 214 )D168 - 214

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