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- PDB-3fzj: TsaR low resolution crystal structure, tetragonal form -

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Basic information

Entry
Database: PDB / ID: 3fzj
TitleTsaR low resolution crystal structure, tetragonal form
ComponentsLysR type regulator of tsaMBCD
KeywordsTranscription regulator / LysR-type / transcriptional regulator / TsaR / LTTR / wHTH
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator TsaR
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.1 Å
AuthorsMonferrer, D. / Tralau, T. / Kertesz, M.A. / Dix, I. / Kikhney, A.G. / Svergun, D.I. / Uson, I.
Citation
Journal: Mol.Microbiol. / Year: 2010
Title: Structural studies on the full-length LysR-type regulator TsaR from Comamonas testosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold.
Authors: Monferrer, D. / Tralau, T. / Kertesz, M.A. / Dix, I. / Sola, M. / Uson, I.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: High crystallizability under air-exclusion conditions of the full-length LysR-type transcriptional regulator TsaR from Comamonas testosteroni T-2 and data-set analysis for a MIRAS structure-solution approach.
Authors: Monferrer, D. / Tralau, T. / Kertesz, M.A. / Panjikar, S. / Uson, I.
History
DepositionJan 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 28, 2025Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_id_ISSN / _citation.title / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LysR type regulator of tsaMBCD
B: LysR type regulator of tsaMBCD
C: LysR type regulator of tsaMBCD
D: LysR type regulator of tsaMBCD
E: LysR type regulator of tsaMBCD
F: LysR type regulator of tsaMBCD
G: LysR type regulator of tsaMBCD
H: LysR type regulator of tsaMBCD
I: LysR type regulator of tsaMBCD
J: LysR type regulator of tsaMBCD


Theoretical massNumber of molelcules
Total (without water)336,43710
Polymers336,43710
Non-polymers00
Water00
1
A: LysR type regulator of tsaMBCD
B: LysR type regulator of tsaMBCD
C: LysR type regulator of tsaMBCD
D: LysR type regulator of tsaMBCD


Theoretical massNumber of molelcules
Total (without water)134,5754
Polymers134,5754
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-95 kcal/mol
Surface area52210 Å2
MethodPISA
2
E: LysR type regulator of tsaMBCD
F: LysR type regulator of tsaMBCD
G: LysR type regulator of tsaMBCD
H: LysR type regulator of tsaMBCD


Theoretical massNumber of molelcules
Total (without water)134,5754
Polymers134,5754
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-93 kcal/mol
Surface area52000 Å2
MethodPISA
3
I: LysR type regulator of tsaMBCD
J: LysR type regulator of tsaMBCD

I: LysR type regulator of tsaMBCD
J: LysR type regulator of tsaMBCD


Theoretical massNumber of molelcules
Total (without water)134,5754
Polymers134,5754
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area11270 Å2
ΔGint-93 kcal/mol
Surface area51820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.370, 204.370, 336.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
LysR type regulator of tsaMBCD / LysR-type transcriptional regulator TsaR


Mass: 33643.727 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: T-2 / Gene: tsar / Plasmid: PQE-70 / Production host: Escherichia coli (E. coli) / Strain (production host): M10 / References: UniProt: P94678
Has protein modificationN
Sequence detailsTHE SEQUENCE OF DATABASE UNIPROTKB/TREMBL P94678 (P94678_COMTE) HAS A SEQUENCING ERROR.THE ...THE SEQUENCE OF DATABASE UNIPROTKB/TREMBL P94678 (P94678_COMTE) HAS A SEQUENCING ERROR.THE ADDITIONAL LEU (RESIDUE 2) AT THE N-TERMINUS OF THE STRUCTURE IS CORRECT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.22 Å3/Da / Density % sol: 76.42 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 2M Ammonium phosphate, 0.1M Tris-HCl, pH 8.5, microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 7→49.57 Å / Num. all: 11860 / Num. obs: 11779 / % possible obs: 99.3 % / Redundancy: 7.73 % / Rmerge(I) obs: 0.1089 / Rsym value: 0.0492 / Net I/σ(I): 17.09
Reflection shellResolution: 7→7.1 Å / Redundancy: 8.15 % / Rmerge(I) obs: 0.6625 / Mean I/σ(I) obs: 2.74 / Num. unique all: 480 / Rsym value: 0.3896 / % possible all: 100

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Processing

Software
NameClassification
PHASERphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FXQ

3fxq


Resolution: 7.1→42.34 Å / Occupancy max: 1 / Occupancy min: 0.5 /
Num. reflection% reflection
all11860 -
obs11779 99.3 %
Displacement parametersBiso max: 46.03 Å2 / Biso mean: 15.571 Å2 / Biso min: 2.58 Å2
Refinement stepCycle: LAST / Resolution: 7.1→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22545 0 0 0 22545

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