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- PDB-2xdn: Transcription factor TtgR H67A mutant -

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Basic information

Entry
Database: PDB / ID: 2xdn
TitleTranscription factor TtgR H67A mutant
ComponentsHTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / 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
HTH-type transcriptional regulator TtgR
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDaniels, C. / Lu, D. / Zhang, X. / Ramos, J.L.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Domain Cross-Talk During Effector Binding to the Multidrug Binding Ttgr Regulator.
Authors: Daniels, C. / Daddaoua, A. / Lu, D. / Zhang, X. / Ramos, J.L.
History
DepositionMay 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2010Provider: 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
C: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR
D: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR


Theoretical massNumber of molelcules
Total (without water)95,2934
Polymers95,2934
Non-polymers00
Water19811
1
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR


Theoretical massNumber of molelcules
Total (without water)47,6472
Polymers47,6472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-18.4 kcal/mol
Surface area17510 Å2
MethodPISA
2
C: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR
D: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR


Theoretical massNumber of molelcules
Total (without water)47,6472
Polymers47,6472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-17.9 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.111, 43.174, 114.803
Angle α, β, γ (deg.)96.93, 99.26, 96.03
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 23823.334 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: DOT-T1E / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9AIU0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 67 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 67 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, HIS 67 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 67 TO ALA ENGINEERED RESIDUE IN CHAIN C, HIS 67 TO ALA ENGINEERED RESIDUE IN CHAIN D, HIS 67 TO ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.56 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9745
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9745 Å / Relative weight: 1
ReflectionResolution: 2.2→41.7 Å / Num. obs: 37118 / % possible obs: 88 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 30.55 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.9 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.739 Å / SU ML: 1.24 / σ(F): 0.02 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2879 1829 5.1 %
Rwork0.2183 --
obs0.2219 36073 88.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.731 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0747 Å2-5.9206 Å21.5813 Å2
2---2.7608 Å2-6.5666 Å2
3---0.6861 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 0 11 6355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086445
X-RAY DIFFRACTIONf_angle_d1.188739
X-RAY DIFFRACTIONf_dihedral_angle_d19.4962345
X-RAY DIFFRACTIONf_chiral_restr0.0721019
X-RAY DIFFRACTIONf_plane_restr0.0051146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25950.36961360.28182264X-RAY DIFFRACTION76
2.2595-2.3260.38111160.25672355X-RAY DIFFRACTION80
2.326-2.4010.33481500.26092489X-RAY DIFFRACTION82
2.401-2.48680.36211180.24952486X-RAY DIFFRACTION85
2.4868-2.58640.3241660.23632593X-RAY DIFFRACTION88
2.5864-2.70410.32841480.23852740X-RAY DIFFRACTION91
2.7041-2.84660.29621450.23132723X-RAY DIFFRACTION93
2.8466-3.02490.31321390.23962781X-RAY DIFFRACTION93
3.0249-3.25840.28891390.23292808X-RAY DIFFRACTION94
3.2584-3.58610.32781390.21882829X-RAY DIFFRACTION93
3.5861-4.10470.25681440.19872684X-RAY DIFFRACTION92
4.1047-5.16990.23051390.17892717X-RAY DIFFRACTION91
5.1699-41.74650.22511500.18472775X-RAY DIFFRACTION93

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