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- PDB-2uxh: TtgR in complex with Quercetin -

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Basic information

Entry
Database: PDB / ID: 2uxh
TitleTtgR in complex with Quercetin
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
3,5,7,3',4'-PENTAHYDROXYFLAVONE / HTH-type transcriptional regulator TtgR
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 28, 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)48,3854
Polymers47,7812
Non-polymers6042
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.650, 231.881, 44.330
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 / TOLUENE EFFLUX PUMP TTGABC OPERON REPRESSOR / TRANSCRIPTIONAL REPRESSOR


Mass: 23890.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Cell line (production host): B834 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9AIU0
#2: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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 %
Crystal growpH: 6.5
Details: 0.2 M MGCL2, 0.1 M BIS-TRIS PH 6.5, 25% (V/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16721 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5
Reflection shellHighest resolution: 2.4 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.32 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.869 / SU B: 26.52 / SU ML: 0.273 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.902 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1273 7.6 %RANDOM
Rwork0.237 ---
obs0.242 15448 84.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2---1.42 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 44 191 3435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213296
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9744472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11223.165158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.94215559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2211536
X-RAY DIFFRACTIONr_chiral_restr0.1590.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.21834
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22258
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3590.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.63522105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9271.53245
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.64121358
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8011.51227
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: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 68 -
Rwork0.301 924 -
obs--68.13 %
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)
18.52262.3782-1.71397.3317-2.75785.1115-0.0471-0.6501-0.50460.3115-0.11540.61830.29270.01080.16250.0091-0.02610.0902-0.20330.0615-0.0613-1.381310.509619.7197
22.7160.4223-0.8364.4186-0.66292.89490.345-0.13310.32840.3637-0.30250.4326-0.4627-0.1581-0.0425-0.03180.02710.0262-0.1889-0.0329-0.17521.737736.409312.1132
37.7618-2.6908-4.99626.23811.97186.3661-0.12780.3603-0.9908-0.6403-0.4757-0.21660.9237-0.04420.60350.08470.15880.2086-0.1708-0.0552-0.091916.35429.9217-11.0734
42.77110.4342-0.77594.31780.39452.93590.17120.20750.1884-0.4255-0.2102-0.3434-0.43940.09880.039-0.01130.02650.0152-0.18790.1145-0.20715.185135.8377-2.6709
513.00254.940815.50517.80266.257718.51210.4207-0.44190.11240.5514-2.12360.05220.2442-1.17321.70290.0012-0.0004-0.0006-0.00120.0007-0.00088.257135.79414.8863
60.63090.1904-0.46540.4932-0.0350.89910.00430.06220.03680.0245-0.0489-0.0581-0.15460.01120.0446-0.147-0.0028-0.05780.28190.03690.19038.95931.88233.6476
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 - 2107
8X-RAY DIFFRACTION6B2001 - 2084

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