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- PDB-1v96: Crystal structure of hypothetical protein of unknown function fro... -

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Basic information

Entry
Database: PDB / ID: 1v96
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 / 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 / MAD / Resolution: 1.75 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
DepositionJan 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6975
Polymers34,4212
Non-polymers2763
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-30 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.909, 95.463, 102.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHIANS (A AND B). BILOGICAL UNIT IS A DIMER

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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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.88 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6.4% PEG 4000, 0.1M CITRATE, pH 6.0, 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: 0.9792, 0.9795, 1.0000
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 23, 2003 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
311
ReflectionResolution: 1.75→30 Å / Num. obs: 45126 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.039
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.199 / Num. unique all: 45126 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.75→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHTOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: DISORDER RESIDUES IN CHAIN A FROM A52-A56
RfactorNum. reflectionSelection details
Rfree0.228 3139 RANDOM
Rwork0.209 --
obs0.209 44322 -
all-45309 -
Displacement parametersBiso mean: 33.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 18 365 2728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.285 505 -
Rwork0.261 --
obs--95.9 %

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