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- PDB-2dbb: Crystal structure of PH0061 -

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Basic information

Entry
Database: PDB / ID: 2dbb
TitleCrystal structure of PH0061
ComponentsPutative HTH-type transcriptional regulator PH0061
KeywordsTRANSCRIPTIONAL REGULATOR / AsnC family / helix-turn-helix (HTH) domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Winged helix-turn-helix DNA-binding / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Winged helix-turn-helix DNA-binding / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized HTH-type transcriptional regulator PH0061
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsNishino, A. / Hosaka, T. / Murayama, K. / Shirouzu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH0061
Authors: Hosaka, T. / Nishino, A. / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 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

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Assembly

Deposited unit
A: Putative HTH-type transcriptional regulator PH0061
B: Putative HTH-type transcriptional regulator PH0061


Theoretical massNumber of molelcules
Total (without water)35,2422
Polymers35,2422
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-17 kcal/mol
Surface area14770 Å2
MethodPISA
2
A: Putative HTH-type transcriptional regulator PH0061
B: Putative HTH-type transcriptional regulator PH0061

A: Putative HTH-type transcriptional regulator PH0061
B: Putative HTH-type transcriptional regulator PH0061


Theoretical massNumber of molelcules
Total (without water)70,4844
Polymers70,4844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area15160 Å2
ΔGint-49 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.330, 118.810, 132.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Putative HTH-type transcriptional regulator PH0061 / hypothetical protein / PH0061


Mass: 17620.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pRARE / References: UniProt: O57802
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2M Sodium citrate, 0.5% Ethyl Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97900, 0.97929, 0.964
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 29, 2005 / Details: mirrors
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979291
30.9641
ReflectionResolution: 2→50 Å / Num. obs: 24083 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.081 / Net I/σ(I): 14.74
Reflection shellResolution: 2→2.09 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 24083 / Rsym value: 0.314 / % possible all: 70.4

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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→50 Å / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1717 -RANDAM
Rwork0.198 ---
obs-20234 75.5 %-
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1-10 Å20 Å20 Å2
2---0.9 Å20 Å2
3----9.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 0 92 2497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2→2.13 Å
RfactorNum. reflection
Rfree0.291 144
Rwork0.243 -
obs-2853

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