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- PDB-1ye5: Crystal structure of hypothetical protein of unknown function fro... -

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Basic information

Entry
Database: PDB / ID: 1ye5
TitleCrystal structure of hypothetical protein of unknown function from pyrococcus horikoshii OT3
Componentshypothetical protein PH0500
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ROSSMANN FOLD / TRNA SYNTHETASE / NUCLEOTIDE BINDING PROTEIN / PIN DOMAIN / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Probable ribonuclease VapC, Thermococci / : / VapC family / 5'-nuclease / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJeyakanthan, J. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.
Authors: Jeyakanthan, J. / Inagaki, E. / Kuroishi, C. / Tahirov, T.H.
History
DepositionDec 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 PH0500
B: hypothetical protein PH0500


Theoretical massNumber of molelcules
Total (without water)34,4212
Polymers34,4212
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-24 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.342, 46.381, 62.484
Angle α, β, γ (deg.)90.00, 113.33, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE CRYSTALLOGRAPHY ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHAINS (A AND B). BIOLOGICAL UNITS IS A HOMODIMER

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Components

#1: Protein hypothetical protein PH0500


Mass: 17210.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODON PLUS (DE3)-RIL / References: UniProt: O58236
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.1 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 12.5% PEG 4000, 0.1M MES BUFFER, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 26, 2003 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 18805 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.21 / Num. unique all: 18805 / % possible all: 95.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V96

1v96


Resolution: 2→19.48 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 926739.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1231 6.8 %RANDOM
Rwork0.234 ---
obs0.234 18036 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.0083 Å2 / ksol: 0.372262 e/Å3
Displacement parametersBiso mean: 22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 0 217 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.444 193 7.3 %
Rwork0.407 2450 -
obs--82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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