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- PDB-2xro: Crystal structure of TtgV in complex with its DNA operator -

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Basic information

Entry
Database: PDB / ID: 2xro
TitleCrystal structure of TtgV in complex with its DNA operator
Components
  • (TTGV OPERATOR DNA) x 2
  • HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV
KeywordsDNA-BINDING PROTEIN/DNA / DNA-BINDING PROTEIN-DNA COMPLEX / TETRAMERIC GENE REGULATOR / COOPERATIVE DNA BINDING / MULTIDRUG BINDING PROTEIN / ANTIBIOTIC RESISTANCE / COMPLEX (DNA-BINDING PROTEIN-DNA )
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative 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
OSMIUM ION / DNA / DNA (> 10) / HTH-type transcriptional regulator TtgV
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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 TTGV
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV
E: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV
F: HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV
X: TTGV OPERATOR DNA
Y: TTGV OPERATOR DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9708
Polymers128,5896
Non-polymers3802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19510 Å2
ΔGint-139.9 kcal/mol
Surface area51790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.584, 89.584, 416.747
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 14:253 )
211CHAIN F AND (RESSEQ 14:253 )
112CHAIN A AND (RESSEQ 15:253 )
212CHAIN E AND (RESSEQ 15:253 )

NCS ensembles :
ID
1
2

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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.: 4 / 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: DNA chain TTGV OPERATOR DNA


Mass: 12818.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS PUTIDA (bacteria)
#3: DNA chain TTGV OPERATOR DNA


Mass: 13344.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS PUTIDA (bacteria)
#4: Chemical ChemComp-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Os
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 ENGINEERED RESIDUE IN CHAIN E, CYS 109 TO SER ENGINEERED RESIDUE IN CHAIN E, CYS 205 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 109 TO SER ENGINEERED RESIDUE IN CHAIN F, 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: 3.76 Å3/Da / Density % sol: 67.32 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.1409
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1409 Å / Relative weight: 1
ReflectionResolution: 3.4→77.5 Å / Num. obs: 25878 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 116.71 Å2 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XRN

2xrn


Resolution: 3.4→62.225 Å / SU ML: 0.43 / σ(F): 1.94 / Phase error: 29.65 / Stereochemistry target values: ML
Details: B_SOL IS 102. NO SIGMA CUTOFF WAS APPLIED TO THE DATA. FULL ANOMALOUS DATA USED FOR FIT TO DATA STATISTICS.
RfactorNum. reflection% reflection
Rfree0.2823 1316 5 %
Rwork0.2139 --
obs0.217 25878 92.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.258 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.9817 Å20 Å20 Å2
2---12.9817 Å20 Å2
3---25.9635 Å2
Refinement stepCycle: LAST / Resolution: 3.4→62.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7102 1736 2 0 8840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019435
X-RAY DIFFRACTIONf_angle_d1.23812753
X-RAY DIFFRACTIONf_dihedral_angle_d19.4843505
X-RAY DIFFRACTIONf_chiral_restr0.0651552
X-RAY DIFFRACTIONf_plane_restr0.0031334
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1780X-RAY DIFFRACTIONPOSITIONAL
12F1780X-RAY DIFFRACTIONPOSITIONAL0.014
21A1768X-RAY DIFFRACTIONPOSITIONAL
22E1768X-RAY DIFFRACTIONPOSITIONAL0.008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.52150.36592200.31734104X-RAY DIFFRACTION84
3.5215-3.66250.31842520.28684170X-RAY DIFFRACTION86
3.6625-3.82910.3171780.2684366X-RAY DIFFRACTION89
3.8291-4.0310.32432590.25934460X-RAY DIFFRACTION91
4.031-4.28350.29512760.21954485X-RAY DIFFRACTION92
4.2835-4.61410.26092290.20774590X-RAY DIFFRACTION94
4.6141-5.07820.32512350.20864691X-RAY DIFFRACTION96
5.0782-5.81260.26772420.20714813X-RAY DIFFRACTION98
5.8126-7.32140.26482280.19814942X-RAY DIFFRACTION100
7.3214-62.23560.24081790.18574709X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -24.8937 Å / Origin y: 37.406 Å / Origin z: -34.9819 Å
111213212223313233
T0.1499 Å2-0.3391 Å2-0.0409 Å2-0.5345 Å20.031 Å2--0.1238 Å2
L1.8457 °2-0.1525 °20.7888 °2-2.0483 °2-1.3185 °2--2.1531 °2
S-0.0888 Å °-0.1243 Å °-0.0831 Å °-0.09 Å °-0.0016 Å °0.1445 Å °0.0927 Å °-0.158 Å °0.0293 Å °
Refinement TLS groupSelection details: ALL

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