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- PDB-1uly: Crystal structure analysis of the ArsR homologue DNA-binding prot... -

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Basic information

Entry
Database: PDB / ID: 1uly
TitleCrystal structure analysis of the ArsR homologue DNA-binding protein from P. horikoshii OT3
Componentshypothetical protein PH1932
KeywordsDNA BINDING PROTEIN / helix-turn-helix / structural genomics
Function / homology
Function and homology information


protein heterodimerization activity / DNA-binding transcription factor activity
Similarity search - Function
Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Histone, subunit A / Histone, subunit A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Histone-fold / Arc Repressor Mutant, subunit A ...Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Histone, subunit A / Histone, subunit A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Histone-fold / 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: 2.5 Å
AuthorsItou, H. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of the PH1932 protein, a unique archaeal ArsR type winged-HTH transcription factor from Pyrococcus horikoshii OT3
Authors: Itou, H. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionSep 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PH1932


Theoretical massNumber of molelcules
Total (without water)23,0821
Polymers23,0821
Non-polymers00
Water45025
1
A: hypothetical protein PH1932

A: hypothetical protein PH1932


Theoretical massNumber of molelcules
Total (without water)46,1642
Polymers46,1642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area4190 Å2
ΔGint-33.3 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.640, 90.640, 132.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein hypothetical protein PH1932 / ArsR homologue protein


Mass: 23081.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1932 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: O59595
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG400, HEPES, magnesium chloride, glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792, 0.9795, 0.9685
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
30.96851
ReflectionResolution: 2.5→40 Å / Num. obs: 7284 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.295 / Num. unique all: 699 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 710 -RANDOM
Rwork0.204 ---
all-7284 --
obs-7284 99.4 %-
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å24.41 Å20 Å2
2---2.4 Å20 Å2
3---4.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 0 25 1605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.308 112 -
Rwork0.244 --
obs-1053 97.2 %

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