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- PDB-3vpr: Crystal Structure of a TetR Family Transcriptional Regulator PfmR... -

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Basic information

Entry
Database: PDB / ID: 3vpr
TitleCrystal Structure of a TetR Family Transcriptional Regulator PfmR from Thermus thermophilus HB8
ComponentsTranscriptional regulator, TetR familyTranscriptional regulation
KeywordsDNA BINDING PROTEIN / All Alpha / Helix-Turn-Helix / Transcriptional Repressor
Function / homology
Function and homology information


DNA binding / identical protein binding
Similarity search - Function
HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, 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. ...HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, 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 regulator, TetR family
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å
AuthorsAgari, Y. / Sakamoto, K. / Kuramitsu, S. / Shinkai, A.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Transcriptional repression mediated by a TetR family protein, PfmR, from Thermus thermophilus HB8
Authors: Agari, Y. / Sakamoto, K. / Kuramitsu, S. / Shinkai, A.
History
DepositionMar 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
C: Transcriptional regulator, TetR family
D: Transcriptional regulator, TetR family


Theoretical massNumber of molelcules
Total (without water)87,4734
Polymers87,4734
Non-polymers00
Water2,702150
1
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family


Theoretical massNumber of molelcules
Total (without water)43,7372
Polymers43,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-22 kcal/mol
Surface area17910 Å2
MethodPISA
2
C: Transcriptional regulator, TetR family
D: Transcriptional regulator, TetR family


Theoretical massNumber of molelcules
Total (without water)43,7372
Polymers43,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-19 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.681, 57.584, 133.447
Angle α, β, γ (deg.)90.00, 94.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcriptional regulator, TetR family / Transcriptional regulation / Transcriptional Repressor PfmR


Mass: 21868.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHB023 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q53WD9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100mM Phosphate-citrate, 40% v/v PEG 300, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 5, 2011
Details: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 35016 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.6
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 7.2 / Num. unique all: 2446 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.27→28.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1431664.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3475 9.9 %RANDOM
Rwork0.212 ---
all0.218 ---
obs0.212 34992 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.2844 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.7 Å20 Å20.19 Å2
2--1.67 Å20 Å2
3----8.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.27→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 0 150 6130
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.131.5
X-RAY DIFFRACTIONc_mcangle_it6.262
X-RAY DIFFRACTIONc_scbond_it7.672
X-RAY DIFFRACTIONc_scangle_it9.762.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.27→2.41 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 587 10.2 %
Rwork0.235 5167 -
obs-5754 99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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