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- PDB-2uxp: TtgR in complex Chloramphenicol -

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Basic information

Entry
Database: PDB / ID: 2uxp
TitleTtgR in complex Chloramphenicol
ComponentsHTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR
KeywordsTRANSCRIPTION / DNA-BINDING / TETR FAMILY
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding
Similarity search - Function
Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / 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 ...Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / 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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CHLORAMPHENICOL / HTH-type transcriptional regulator TtgR
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAlguel, Y. / Meng, C. / Teran, W. / Krell, T. / Ramos, J.L. / Gallegos, M.-T. / Zhang, X.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of Multidrug Binding Protein Ttgr in Complex with Antibiotics and Plant Antimicrobials.
Authors: Alguel, Y. / Meng, C. / Teran, W. / Krell, T. / Ramos, J.L. / Gallegos, M.-T. / Zhang, X.
History
DepositionMar 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4274
Polymers47,7812
Non-polymers6462
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.457, 230.673, 44.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR / TRANSCRIPTIONAL REPRESSOR / TOLUENE EFFLUX PUMP TTGABC OPERON REPRESSOR


Mass: 23890.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: DOT-T1E / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9AIU0
#2: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 6.5 / Details: 0.2 M MGCL2, 0.1 M BIS-TRIS PH 6.5, 20%(V/V)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12226 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 37.9
Reflection shellHighest resolution: 2.7 Å / Mean I/σ(I) obs: 5.3 / % possible all: 37.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.55 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.869 / SU B: 33.425 / SU ML: 0.306 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 957 7.8 %RANDOM
Rwork0.232 ---
obs0.237 11309 89.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.17 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å20 Å20 Å2
2---3.58 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 40 109 3314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213257
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.974416
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5195409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.23623.2150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47915546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0941533
X-RAY DIFFRACTIONr_chiral_restr0.180.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.280.21885
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22278
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.061.52090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.89123239
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.53731294
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1524.51177
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 34 -
Rwork0.259 432 -
obs--46.23 %
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)
15.4632.9824-0.39455.2072-0.31040.98780.0022-0.3731-0.2540.4163-0.07270.17860.09280.02080.0705-0.0913-0.01260.0607-0.13340.0757-0.0775-1.459510.422219.7671
20.9114-0.2611-0.67041.84590.33252.16230.1418-0.01550.0394-0.0476-0.15690.1371-0.3458-0.07170.0151-0.03020.0553-0.0352-0.15380.0019-0.15931.716436.173112.1636
34.0901-0.5899-4.44633.882-0.53215.7867-0.52580.0926-0.7053-0.3442-0.38060.00211.14960.28420.9064-0.00190.13440.1925-0.03740.0013-0.063716.103510.0192-10.6312
40.58740.624-0.43951.7518-0.33871.90480.06110.0689-0.0835-0.1222-0.0669-0.1372-0.31270.10440.0058-0.0428-0.0245-0.0001-0.14250.0336-0.133715.03635.5851-2.5443
547.54271.6777-52.02810.0644-1.62565.4543-1.329-2.37571.5538-0.62481.6533-0.05644.82021.3137-0.3242-0.0091-0.1752-0.04160.00040.16070.03157.836135.86195.0408
60.28190.1316-0.08750.14890.24990.9928-0.00270.03930.0845-0.016-0.0301-0.0166-0.0526-0.06090.03280.4130.0264-0.04840.56630.04760.50847.084429.13334.823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B6 - 53
2X-RAY DIFFRACTION2B54 - 210
3X-RAY DIFFRACTION3A5 - 53
4X-RAY DIFFRACTION4A54 - 210
5X-RAY DIFFRACTION5A1211
6X-RAY DIFFRACTION5B1211
7X-RAY DIFFRACTION6A2001 - 2051
8X-RAY DIFFRACTION6B2001 - 2058

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