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- PDB-1t33: Structural Genomics, The crystal structure of a putative transcri... -

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Basic information

Entry
Database: PDB / ID: 1t33
TitleStructural Genomics, The crystal structure of a putative transcriptional repressor (TetR/AcrR family) from Salmonella typhimurim LT2
Componentsputative transcriptional repressor (TetR/AcrR family)
KeywordsTRANSCRIPTION / Structural genomics / transcriptional repressor / TetR/CcrR family / Helix turn helix DNA binding domain / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Transcription regulator YbiH, C-terminal / HTH-type transcriptional dual regulator CecR, C-terminal domain / 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 YbiH, C-terminal / HTH-type transcriptional dual regulator CecR, C-terminal domain / 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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional repressor (TetR/AcrR family)
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Zhou, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a putative transcriptional repressor (TetR/AcrR family) from Salmonella typhimurium
Authors: Zhang, R. / Zhou, M. / Collart, F. / Joachimiak, A.
History
DepositionApr 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative transcriptional repressor (TetR/AcrR family)
B: putative transcriptional repressor (TetR/AcrR family)


Theoretical massNumber of molelcules
Total (without water)50,2472
Polymers50,2472
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-36 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.630, 122.192, 108.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThis protein existed as dimer, MolA and MolB represent the dimer in the asymmtric unit.

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Components

#1: Protein putative transcriptional repressor (TetR/AcrR family)


Mass: 25123.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: ybiH / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8ZQN9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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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: 3.66 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M sodium acetate, 0.17M ammonium acetate, 10% PEG3350, 15% glycerol, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9798, 0.9465
DetectorType: SBC-2 / Detector: CCD / Date: Mar 2, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.94651
ReflectionResolution: 2.2→50 Å / Num. all: 73727 / Num. obs: 73137 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.2 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.39 / Num. unique all: 6920 / % possible all: 93.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 234120.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3365 4.9 %RANDOM
Rwork0.205 ---
all0.21 72521 --
obs0.205 68025 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5111 Å2 / ksol: 0.361093 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.55 Å20 Å20 Å2
2--6.09 Å20 Å2
3---0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 0 194 3613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 510 5.1 %
Rwork0.305 9532 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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