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- PDB-2wgb: Crystal structure of the TetR-like transcriptional regulator LfrR... -

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Basic information

Entry
Database: PDB / ID: 2wgb
TitleCrystal structure of the TetR-like transcriptional regulator LfrR from Mycobacterium smegmatis
ComponentsTETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
KeywordsTRANSCRIPTION / TETR / LFRR / REPRESSOR / DNA-BINDING / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TetR family transcriptional repressor LfrR
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsBellinzoni, M. / Buroni, S. / Riccardi, G. / De Rossi, E. / Alzari, P.M.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Structural Plasticity and Distinct Drug-Binding Modes of Lfrr, a Mycobacterial Efflux Pump Regulator.
Authors: Bellinzoni, M. / Buroni, S. / Schaeffer, F. / Riccardi, G. / De Rossi, E. / Alzari, P.M.
History
DepositionApr 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
B: TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7836
Polymers41,3992
Non-polymers3844
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-76.48 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.646, 86.646, 96.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR / TRANSCRIPTIONAL REGULATOR LFRR


Mass: 20699.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2155 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58L87
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 8 / Details: 10% PEG8000, 0.5 M LISO4, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→48.4 Å / Num. obs: 25569 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→43.323 Å / SU ML: 0.27 / σ(F): 1.41 / Phase error: 18.89 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAIN ISOTROPIC EQUIVALENTS OF THE SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflection
Rfree0.228 1274 5 %
Rwork0.1853 --
obs0.1874 25510 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.155 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4441 Å20 Å2-0 Å2
2--1.4441 Å20 Å2
3----2.8882 Å2
Refinement stepCycle: LAST / Resolution: 2→43.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 20 169 2629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072591
X-RAY DIFFRACTIONf_angle_d0.8253553
X-RAY DIFFRACTIONf_dihedral_angle_d14.446920
X-RAY DIFFRACTIONf_chiral_restr0.054408
X-RAY DIFFRACTIONf_plane_restr0.004459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.21481410.18382628X-RAY DIFFRACTION100
2.0801-2.17480.19211350.16972639X-RAY DIFFRACTION100
2.1748-2.28940.20571430.16552637X-RAY DIFFRACTION100
2.2894-2.43290.20191370.1652670X-RAY DIFFRACTION100
2.4329-2.62070.20661390.16632667X-RAY DIFFRACTION100
2.6207-2.88440.23651400.17952679X-RAY DIFFRACTION100
2.8844-3.30160.23251420.18672702X-RAY DIFFRACTION100
3.3016-4.15910.23281450.17142729X-RAY DIFFRACTION100
4.1591-43.33310.24311520.212885X-RAY DIFFRACTION100
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)
10.83080.943-0.471.7297-1.10892.0341-0.05250.1393-0.1463-0.30730.103-0.10720.3863-0.0829-0.03450.2281-0.0192-0.01040.1276-0.00520.145334.0243-8.385542.8913
21.18010.09440.16791.60990.12552.20220.02810.07120.12610.062-0.01860.0139-0.06930.0405-0.01440.0173-0.01580.00490.08980.01540.068838.14814.291836.4709
31.0277-0.80930.96290.9341-0.9361.62430.3008-0.0804-0.5816-0.52630.10370.0371.2181.3175-0.1340.60690.3312-0.03650.8129-0.03440.294165.0481-1.756143.0339
43.8028-1.13151.16990.74280.43933.4494-0.1013-0.0250.17680.2748-0.0829-0.09750.05980.31710.16060.1105-0.1023-0.03220.26530.06160.161455.567920.007445.524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 8:53
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 54:185
3X-RAY DIFFRACTION3CHAIN B AND RESSEQ 16:53
4X-RAY DIFFRACTION4CHAIN B AND RESSEQ 54:186

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