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- PDB-1ub9: Structure of the transcriptional regulator homologue protein from... -

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Basic information

Entry
Database: PDB / ID: 1ub9
TitleStructure of the transcriptional regulator homologue protein from Pyrococcus horikoshii OT3
ComponentsHypothetical protein PH1061
KeywordsTRANSCRIPTION / helix-turn-helix motif / winged helix motif / STRUCTURAL GENOMICS
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Winged helix DNA-binding domain / Winged helix DNA-binding domain / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH arsR-type domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsOkada, U. / Sakai, N. / Tajika, Y. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: Proteins / Year: 2006
Title: Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3.
Authors: Okada, U. / Sakai, N. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionApr 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: Hypothetical protein PH1061


Theoretical massNumber of molelcules
Total (without water)11,4031
Polymers11,4031
Non-polymers00
Water1,02757
1
A: Hypothetical protein PH1061

A: Hypothetical protein PH1061


Theoretical massNumber of molelcules
Total (without water)22,8052
Polymers22,8052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2580 Å2
ΔGint-31 kcal/mol
Surface area10670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)45.159, 45.159, 96.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-155-

HOH

DetailsThe biological assembly is a dimer by the operation: y, x,-z.

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Components

#1: Protein Hypothetical protein PH1061 / transcriptional regulator homologue protein


Mass: 11402.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1061 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)Codon+ / References: UniProt: O58788
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.94 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: ammonium phosphate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9000,0.9794,0.9796
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2003 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97941
30.97961
ReflectionResolution: 2.05→33 Å / Num. all: 6696 / Num. obs: 6696 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 14 % / Rmerge(I) obs: 0.234 / Num. unique all: 635 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.05→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 645 9 %RANDOM
Rwork0.216 ---
all-6591 --
obs-6591 99.3 %-
Solvent computationBsol: 55.8 Å2 / ksol: 0.3944 e/Å3
Displacement parametersBiso mean: 39.37 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å20 Å2
2---5.18 Å20 Å2
3---10.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms799 0 0 57 856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006715
X-RAY DIFFRACTIONc_angle_deg1.22058
X-RAY DIFFRACTIONc_dihedral_angle_d18.97157
X-RAY DIFFRACTIONc_improper_angle_d0.96676
X-RAY DIFFRACTIONc_mcbond_it1.598
X-RAY DIFFRACTIONc_mcangle_it2.527
X-RAY DIFFRACTIONc_scbond_it2.926
X-RAY DIFFRACTIONc_scangle_it4.043
LS refinement shellResolution: 2.05→2.12 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.284 65 10.2 %
Rwork0.228 537 -
obs-602 94.8 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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