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- PDB-3vuq: Crystal structure of TTHA0167, a transcriptional regulator, TetR/... -

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Basic information

Entry
Database: PDB / ID: 3vuq
TitleCrystal structure of TTHA0167, a transcriptional regulator, TetR/AcrR family from Thermus thermophilus HB8
ComponentsTranscriptional regulator (TetR/AcrR family)
KeywordsTRANSCRIPTION REGULATOR / helix-turn-helix / transcriptional regulator / DNA Binding
Function / homology
Function and homology information


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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator (TetR/AcrR family)
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsAgari, Y. / Sakamoto, K. / Agari, K. / Kuramitsu, S. / Shinkai, A.
CitationJournal: Proteins / Year: 2013
Title: Structure and function of a TetR family transcriptional regulator, SbtR, from thermus thermophilus HB8
Authors: Agari, Y. / Sakamoto, K. / Yutani, K. / Kuramitsu, S. / Shinkai, A.
History
DepositionJul 4, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator (TetR/AcrR family)
B: Transcriptional regulator (TetR/AcrR family)
C: Transcriptional regulator (TetR/AcrR family)
D: Transcriptional regulator (TetR/AcrR family)


Theoretical massNumber of molelcules
Total (without water)85,4884
Polymers85,4884
Non-polymers00
Water5,332296
1
A: Transcriptional regulator (TetR/AcrR family)
B: Transcriptional regulator (TetR/AcrR family)


Theoretical massNumber of molelcules
Total (without water)42,7442
Polymers42,7442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-25 kcal/mol
Surface area18690 Å2
MethodPISA
2
C: Transcriptional regulator (TetR/AcrR family)
D: Transcriptional regulator (TetR/AcrR family)


Theoretical massNumber of molelcules
Total (without water)42,7442
Polymers42,7442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-25 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.327, 174.821, 56.158
Angle α, β, γ (deg.)90.00, 92.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcriptional regulator (TetR/AcrR family) / TTHA0167


Mass: 21371.908 Da / Num. of mol.: 4 / Fragment: UNP residues 3-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0167 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLX6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5451.63
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931microbatch4.630% PEG300, 0.2M phosphate citrate, 0.15M lithium chloride, pH 4.6, micro-batch, temperature 293.0K
2932microbatch4.230% PEG300, 0.2 M phosphate citrate, pH 4.2, micro-batch, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2009
Details: a fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror
RadiationMonochromator: fixed exit Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 53147 / % possible obs: 98.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.1
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 5.77 / Num. unique all: 3090 / % possible all: 79.1

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.05→30.32 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1839630.28 / 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
Rfree0.25 5271 10.1 %RANDOM
Rwork0.201 ---
obs0.201 52190 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.6429 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20.27 Å2
2--0.26 Å20 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å-0.03 Å
Refinement stepCycle: LAST / Resolution: 2.05→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5767 0 0 296 6063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d17.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.031.5
X-RAY DIFFRACTIONc_mcangle_it7.262
X-RAY DIFFRACTIONc_scbond_it8.942
X-RAY DIFFRACTIONc_scangle_it11.332.5
LS refinement shellResolution: 2.05→2.17 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 707 9.8 %
Rwork0.206 6542 -
obs-7249 80.8 %
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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