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- PDB-5nz0: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -

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Basic information

Entry
Database: PDB / ID: 5nz0
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with linezolid
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / EthR / represor / boosting effect
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-ZLD / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.825 Å
AuthorsBlaszczyk, M. / Mendes, V. / Nikiforov, P.O. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: To Be Published
Title: The antibiotics linezolid and sutezolid are ligands for Mycobacterium tuberculosis EthR
Authors: Nikiforov, P.O. / Blaszczyk, M. / Mendes, V. / Boshoff, H.I. / Barry, C.E. / Blundell, T.L. / Abell, C.
History
DepositionMay 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,6593
Polymers25,2591
Non-polymers3992
Water2,234124
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3176
Polymers50,5192
Non-polymers7994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3020 Å2
ΔGint-18 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.382, 121.382, 33.780
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-415-

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-ZLD / N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide / Linezolid / Linezolid


Mass: 337.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20FN3O4 / Comment: antibiotic*YM
#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.: 124 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
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: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.825→121.382 Å / Num. all: 23173 / Num. obs: 23173 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 27.43 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.114 / Rsym value: 0.108 / Net I/av σ(I): 4.5 / Net I/σ(I): 16.1 / Num. measured all: 337554
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value
1.825-1.9213.31.0940.70.3181.1741.094
1.92-2.0415.80.6481.20.1720.6890.648
2.04-2.1815.80.3772.10.10.3990.377
2.18-2.3615.20.2662.90.0720.2820.266
2.36-2.5814.80.1714.40.0470.1810.171
2.58-2.8913.50.126.10.0340.1280.12
2.89-3.3315.10.08580.0230.090.085
3.33-4.0814.10.0669.10.0180.070.066
4.08-5.7712.40.06290.0180.0660.062
5.77-121.38213.90.0597.70.0160.0620.059

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.825→20.23 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.88 / Phase error: 19.54
RfactorNum. reflection% reflection
Rfree0.2195 1184 5.13 %
Rwork0.1842 --
obs0.186 23088 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.05 Å2 / Biso mean: 38.4068 Å2 / Biso min: 12.56 Å2
Refinement stepCycle: final / Resolution: 1.825→20.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 28 124 1626
Biso mean--58.7 46.63 -
Num. residues----190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061540
X-RAY DIFFRACTIONf_angle_d0.7972099
X-RAY DIFFRACTIONf_chiral_restr0.045239
X-RAY DIFFRACTIONf_plane_restr0.004273
X-RAY DIFFRACTIONf_dihedral_angle_d16.797914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8248-1.90780.29681630.278226512814
1.9078-2.00830.26741500.230426732823
2.0083-2.1340.23621650.186726882853
2.134-2.29850.21321350.18726972832
2.2985-2.52950.21251470.171627232870
2.5295-2.89460.2021210.178227602881
2.8946-3.64340.23021490.175127792928
3.6434-20.23160.20261540.17929333087
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)
16.44651.5329-3.26098.158-0.0478.2649-0.00750.94850.3969-0.4720.1123-0.01220.3281-0.307-0.04130.24310.1454-0.0150.43570.02820.339-51.135624.2891-14.5675
27.0326-0.25860.78730.54750.71243.78410.07270.33450.9815-0.1693-0.11-0.3254-0.28590.1583-0.07910.25690.2906-0.00810.557-0.12660.46-58.631228.453-9.7656
37.7639-5.1529-0.33138.49241.11193.9819-0.0691-0.583-0.54010.02650.13890.57970.4342-0.8628-0.07330.173-0.09720.02690.4687-0.02380.2191-40.105412.649-5.3413
44.8692-2.2080.85645.8240.05473.09090.0204-0.09850.12260.16260.0230.05730.0257-0.3743-0.05710.193-0.07960.02180.2902-0.0220.2296-31.827214.3907-11.321
56.2261-2.00351.30132.8223-0.72553.51940.0414-0.3767-0.12590.2176-0.03690.05080.2444-0.3522-0.0330.2475-0.11230.00260.2446-0.01710.1699-26.309313.32231.5718
61.94310.32160.23922.411-0.56993.831-0.00630.0549-0.0308-0.1220.03590.06750.0622-0.1646-0.02060.1638-0.0476-0.00920.1415-0.00910.1648-22.515716.3856-11.2218
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 98 )A68 - 98
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 129 )A99 - 129
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 167 )A130 - 167
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 214 )A168 - 214

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