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- PDB-2xrn: Crystal structure of TtgV -

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Basic information

Entry
Database: PDB / ID: 2xrn
TitleCrystal structure of TtgV
ComponentsHTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / TETRAMER GENE REGULATOR / COOPERATIVE DNA BINDING / MULTIDRUG BINDING PROTEIN / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase ...helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator TtgV
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLu, D. / Fillet, S. / Meng, C. / Alguel, Y. / Kloppsteck, P. / Bergeron, J. / Krell, T. / Gallegos, M.-T. / Ramos, J. / Zhang, X.
CitationJournal: Genes Dev. / Year: 2010
Title: Crystal Structure of Ttgv in Complex with its DNA Operator Reveals a General Model for Cooperative DNA Binding of Tetrameric Gene Regulators.
Authors: Lu, D. / Fillet, S. / Meng, C. / Alguel, Y. / Kloppsteck, P. / Bergeron, J. / Krell, T. / Gallegos, M.T. / Ramos, J. / Zhang, X.
History
DepositionSep 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV


Theoretical massNumber of molelcules
Total (without water)51,2132
Polymers51,2132
Non-polymers00
Water1267
1
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV

A: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV


Theoretical massNumber of molelcules
Total (without water)102,4264
Polymers102,4264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area10850 Å2
ΔGint-59.9 kcal/mol
Surface area39050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.862, 116.184, 71.881
Angle α, β, γ (deg.)90.00, 104.34, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 15:253 )
211CHAIN B AND (RESSEQ 15:253 )

NCS oper: (Code: given
Matrix: (0.240939, 0.000269, -0.97054), (-0.003886, -0.999992, -0.001242), (-0.970532, 0.004071, -0.240936)
Vector: -26.8252, 60.2082, -34.491)

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Components

#1: Protein HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV / TOLUENE TOLERANCE PUMP TTGGHI OPERON REPRESSOR


Mass: 25606.568 Da / Num. of mol.: 2 / Fragment: RESIDUES 14-253 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q93PU6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 109 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 205 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 109 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 205 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 109 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 205 TO SER
Sequence detailsSER 13 IS THE RESULT OF CLONING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.05 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9695
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9695 Å / Relative weight: 1
ReflectionResolution: 2.9→69 Å / Num. obs: 12547 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 57.15 Å2 / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→44.609 Å / SU ML: 0.45 / σ(F): 1.42 / Phase error: 30.16 / Stereochemistry target values: ML
Details: NO SIGMA CUTOFF WAS APPLIED TO THE DATA. FULL ANOMALOUS DATA USED IN FIT TO DATA STATISTICS.
RfactorNum. reflection% reflection
Rfree0.279 629 5 %
Rwork0.2123 --
obs0.2156 12547 92.85 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.137 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3387 Å20 Å29.9073 Å2
2--1.7304 Å20 Å2
3----3.0692 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 0 7 3558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053593
X-RAY DIFFRACTIONf_angle_d0.9864879
X-RAY DIFFRACTIONf_dihedral_angle_d15.3221327
X-RAY DIFFRACTIONf_chiral_restr0.067609
X-RAY DIFFRACTIONf_plane_restr0.003625
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1761X-RAY DIFFRACTIONPOSITIONAL
12B1761X-RAY DIFFRACTIONPOSITIONAL0.117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.03210.39911330.35082676X-RAY DIFFRACTION91
3.0321-3.19190.33631390.25392672X-RAY DIFFRACTION91
3.1919-3.39180.27761180.24072738X-RAY DIFFRACTION92
3.3918-3.65360.32981200.24632686X-RAY DIFFRACTION92
3.6536-4.0210.30141490.22652725X-RAY DIFFRACTION93
4.021-4.60240.28011560.18392720X-RAY DIFFRACTION93
4.6024-5.79650.26541400.18422769X-RAY DIFFRACTION94
5.7965-44.61430.21091530.17312772X-RAY DIFFRACTION95

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