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- PDB-5ovy: Crystal structure of MAB_4384 tetR -

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Basic information

Entry
Database: PDB / ID: 5ovy
TitleCrystal structure of MAB_4384 tetR
ComponentsPutative transcriptional regulator, TetR family
KeywordsDNA BINDING PROTEIN / TetR / efflux pump regulation / antibiotic resistance
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsRichard, M. / Gutierrez, A.V. / Viljoen, A. / Ghigo, E. / Blaise, M. / Kremer, L.
CitationJournal: Front Microbiol / Year: 2018
Title: Mechanistic and Structural Insights Into the Unique TetR-Dependent Regulation of a Drug Efflux Pump inMycobacterium abscessus.
Authors: Richard, M. / Gutierrez, A.V. / Viljoen, A.J. / Ghigo, E. / Blaise, M. / Kremer, L.
History
DepositionAug 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Putative transcriptional regulator, TetR family
A: Putative transcriptional regulator, TetR family


Theoretical massNumber of molelcules
Total (without water)49,5602
Polymers49,5602
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-22 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.800, 100.820, 56.090
Angle α, β, γ (deg.)90.00, 105.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative transcriptional regulator, TetR family


Mass: 24779.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the first G is from expression Tag
Source: (gene. exp.) Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: MAB_4384 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 rosetta 2 pLyS / References: UniProt: B1MJU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM cacodylate pH6.5, 0,2 M MgCl2, 16 pourcent PEG 8000, 5 pourcent dimethylsulfoxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→36.58 Å / Num. obs: 31705 / % possible obs: 92.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 33.91 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.09
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 3193 / % possible all: 93.44

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→36.58 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.25
RfactorNum. reflection% reflection
Rfree0.2135 2000 6.31 %
Rwork0.1847 --
obs0.1865 31696 92.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 0 282 3449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023237
X-RAY DIFFRACTIONf_angle_d0.4524367
X-RAY DIFFRACTIONf_dihedral_angle_d14.3451935
X-RAY DIFFRACTIONf_chiral_restr0.034467
X-RAY DIFFRACTIONf_plane_restr0.003584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94760.34311460.31482165X-RAY DIFFRACTION93
1.9476-2.00020.34251430.29832130X-RAY DIFFRACTION94
2.0002-2.05910.33721460.27172158X-RAY DIFFRACTION94
2.0591-2.12550.30151420.2382105X-RAY DIFFRACTION93
2.1255-2.20150.28671380.23112062X-RAY DIFFRACTION90
2.2015-2.28960.261470.21082180X-RAY DIFFRACTION95
2.2896-2.39380.24161470.20742186X-RAY DIFFRACTION95
2.3938-2.520.23011460.18732156X-RAY DIFFRACTION94
2.52-2.67780.22681380.19812046X-RAY DIFFRACTION89
2.6778-2.88450.23861470.22189X-RAY DIFFRACTION95
2.8845-3.17470.21011430.19542127X-RAY DIFFRACTION93
3.1747-3.63370.18321400.16742066X-RAY DIFFRACTION90
3.6337-4.57670.17271430.1442136X-RAY DIFFRACTION92
4.5767-36.84430.17081340.15751990X-RAY DIFFRACTION85
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)
10.96580.1605-1.10310.6868-0.18185.0979-0.07040.1717-0.0181-0.12440.0416-0.04430.22780.14340.02150.2206-0.00710.0070.20750.00190.2538-11.97413.6533-9.1289
22.4321-0.47890.8845.9626-1.00064.8097-0.0140.15840.03510.005-0.0329-0.3002-0.04680.21730.05640.13840.00250.01890.1797-0.02650.2336-18.789517.011-0.6172
39.24721.01466.53414.9997-0.38714.80480.144-0.6067-0.13460.0485-0.02030.30650.4649-0.8199-0.34880.2689-0.04130.03440.31730.02270.3928-30.50766.27635.7824
43.1604-4.15032.01115.8497-1.25298.9522-0.1529-0.32130.1099-0.37180.00270.5057-0.6636-1.10680.1470.34460.0022-0.08370.47-0.02930.4336-44.666928.9666-19.2571
51.94860.26772.80642.44831.16378.9934-0.22790.05080.0122-0.16690.19470.2783-0.6104-0.30470.01030.2197-0.00060.01790.23730.02780.3473-38.017531.6754-6.1162
61.3864-0.46961.49764.495-2.5523.6888-0.10680.13570.12220.12880.0399-0.0096-0.54580.08890.03360.20620.00460.05320.27910.00240.2902-28.858932.2149-0.7169
75.16571.57270.3196.1995-0.00993.5984-0.0209-0.07440.15720.06090.0940.0393-0.23-0.0032-0.08570.17790.0599-0.00030.15010.01590.2577-25.202621.4022.0639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 11 through 152 )
2X-RAY DIFFRACTION2chain 'B' and (resid 153 through 189 )
3X-RAY DIFFRACTION3chain 'B' and (resid 190 through 212 )
4X-RAY DIFFRACTION4chain 'A' and (resid 14 through 46 )
5X-RAY DIFFRACTION5chain 'A' and (resid 47 through 104 )
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 153 )
7X-RAY DIFFRACTION7chain 'A' and (resid 154 through 213 )

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