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- PDB-2uxu: TtgR in complex with Naringenin -

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Basic information

Entry
Database: PDB / ID: 2uxu
TitleTtgR in complex with Naringenin
ComponentsHTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR
KeywordsTRANSCRIPTION / REPRESSOR PROTEIN / TRANSCRIPTION REGULATION / MULTIDRUG BINDING PROTEIN / TRANSCRIPTIONAL REGULATOR OF EFFLUX PUMPS / REPRESSOR / TETR FAMILY / DNA-BINDING
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 / TetR-type HTH domain profile. ...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
NARINGENIN / HTH-type transcriptional regulator TtgR
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 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

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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)48,3254
Polymers47,7812
Non-polymers5452
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.640, 230.650, 43.966
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-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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, 15%(V/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9333
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9333 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18368 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.2
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 73

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.98 Å / Cross valid method: THROUGHOUT / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2909 1374 7.5 %RANDOM
Rwork0.24285 ---
obs0.24285 16994 90.87 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 49.679 Å2
Baniso -1Baniso -2Baniso -3
1-5.98 Å20 Å20 Å2
2---3.65 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 40 115 3275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.079
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
Num. reflection% reflection
Rwork656 -
obs-45.63 %
Xplor fileSerial no: 1 / Param file: WATER.PARAM

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