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- PDB-2v57: Crystal structure of the TetR-like transcriptional regulator LfrR... -

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Basic information

Entry
Database: PDB / ID: 2v57
TitleCrystal structure of the TetR-like transcriptional regulator LfrR from Mycobacterium smegmatis in complex with proflavine
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
ISOPROPYL ALCOHOL / PROFLAVIN / TetR family transcriptional repressor LfrR
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionOct 2, 2008Deposition 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
C: TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
D: TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,91314
Polymers82,7984
Non-polymers1,11510
Water6,738374
1
A: TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
B: TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8606
Polymers41,3992
Non-polymers4614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-63.03 kcal/mol
Surface area15920 Å2
MethodPISA
2
C: TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
D: TETR FAMILY TRANSCRIPTIONAL REPRESSOR LFRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0538
Polymers41,3992
Non-polymers6546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-61.55 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.300, 62.440, 70.640
Angle α, β, γ (deg.)63.88, 88.34, 88.13
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN C
112CHAIN B
212CHAIN D

NCS ensembles :
ID
1
2

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Components

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


Mass: 20699.471 Da / Num. of mol.: 4
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-PRL / PROFLAVIN


Mass: 209.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLY1 IS A CLONING ARTIFACT

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6.5 / Details: 2.0 M (NH4)2SO4, 5% ISOPROPANOL, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 10, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→48.3 Å / Num. obs: 56578 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.27 Å / SU ML: 0.3 / σ(F): 1.28 / Phase error: 22.83 / 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
Rfree0.234 5297 5 %
Rwork0.196 --
obs0.198 105612 90.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.69 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6927 Å20.2268 Å2-0.2884 Å2
2--5.3277 Å26.3332 Å2
3----2.6351 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 70 374 5742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085509
X-RAY DIFFRACTIONf_angle_d1.0097523
X-RAY DIFFRACTIONf_dihedral_angle_d14.6781949
X-RAY DIFFRACTIONf_chiral_restr0.076859
X-RAY DIFFRACTIONf_plane_restr0.005972
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1292X-RAY DIFFRACTIONPOSITIONAL
12C1292X-RAY DIFFRACTIONPOSITIONAL0.041
21B1326X-RAY DIFFRACTIONPOSITIONAL
22D1326X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.28281620.27533081X-RAY DIFFRACTION83
1.9216-1.94420.29161650.25753198X-RAY DIFFRACTION87
1.9442-1.96790.25011650.25433138X-RAY DIFFRACTION86
1.9679-1.99280.26741790.24543321X-RAY DIFFRACTION89
1.9928-2.0190.27651660.25113183X-RAY DIFFRACTION86
2.019-2.04670.29221730.23833232X-RAY DIFFRACTION90
2.0467-2.07590.281760.22543267X-RAY DIFFRACTION87
2.0759-2.10690.2221730.21113297X-RAY DIFFRACTION90
2.1069-2.13990.2231750.20133308X-RAY DIFFRACTION88
2.1399-2.17490.25011760.20123273X-RAY DIFFRACTION90
2.1749-2.21240.22781640.20953305X-RAY DIFFRACTION89
2.2124-2.25270.26181780.1973283X-RAY DIFFRACTION91
2.2527-2.2960.27031860.19913413X-RAY DIFFRACTION90
2.296-2.34290.24881650.19113289X-RAY DIFFRACTION90
2.3429-2.39380.20891760.17853332X-RAY DIFFRACTION90
2.3938-2.44950.25581780.193321X-RAY DIFFRACTION90
2.4495-2.51070.23091800.18923412X-RAY DIFFRACTION91
2.5107-2.57860.25891830.18483307X-RAY DIFFRACTION91
2.5786-2.65450.23751790.18923396X-RAY DIFFRACTION92
2.6545-2.74020.25771720.18383386X-RAY DIFFRACTION92
2.7402-2.83810.23481850.19163443X-RAY DIFFRACTION92
2.8381-2.95170.23591810.18663412X-RAY DIFFRACTION93
2.9517-3.0860.22131710.19073405X-RAY DIFFRACTION93
3.086-3.24870.22691860.18023459X-RAY DIFFRACTION93
3.2487-3.45220.20861720.17733441X-RAY DIFFRACTION93
3.4522-3.71860.18771850.16293472X-RAY DIFFRACTION94
3.7186-4.09270.21111840.16953469X-RAY DIFFRACTION95
4.0927-4.68450.19221940.16033502X-RAY DIFFRACTION94
4.6845-5.90030.21451850.19663506X-RAY DIFFRACTION95
5.9003-48.28340.2261830.20573464X-RAY DIFFRACTION94
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)
10.85750.45340.08991.94420.25970.92720.0709-0.02360.03360.0587-0.01130.1193-0.1231-0.0608-00.06430.01620.00880.0544-0.01530.078114.2836-2.7156.2791
21.23090.16190.43690.83080.66241.23220.0401-0.12-0.07070.07690.01110.10630.1453-0.0541-0.00010.0955-0.003-0.00020.12580.03960.149812.6482-15.404324.7593
31.17110.47680.4561.49750.5081.54090.08860.0745-0.0659-0.1017-0.017-0.05750.14890.16620.00010.09250.03860.00080.11150.00460.0926-14.336912.4612-25.8406
41.03250.5126-0.23421.3992-0.24520.53490.0641-0.0297-0.01180.169-0.0176-0.0582-0.00360.1099-00.0703-0.0026-0.00680.1411-0.01120.0736-12.64065.5066-4.3003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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