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- PDB-1v7r: Structure of nucleotide triphosphate pyrophosphatase from pyrococ... -

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Basic information

Entry
Database: PDB / ID: 1v7r
TitleStructure of nucleotide triphosphate pyrophosphatase from pyrococcus horikoshii OT3
Componentshypothetical protein PH1917
KeywordsHYDROLASE / NTPase / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


purine nucleoside triphosphate catabolic process / XTP/dITP diphosphatase / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
dITP/XTP pyrophosphatase / Ham1-like protein / Ham1 family / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes.
Authors: Lokanath, N.K. / Pampa, K.J. / Takio, K. / Kunishima, N.
History
DepositionDec 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PH1917
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4262
Polymers21,2331
Non-polymers1921
Water3,639202
1
A: hypothetical protein PH1917
hetero molecules

A: hypothetical protein PH1917
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8514
Polymers42,4672
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x+1/2,-y+3/2,z+1/21
Unit cell
Length a, b, c (Å)79.013, 93.188, 55.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein hypothetical protein PH1917 / Nucleotide triphosphate pyrophosphatase


Mass: 21233.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: NTPase / Plasmid: PET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: O59580, nucleoside-triphosphate diphosphatase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.41 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.1
Details: 1.6M Tris sodium citrate, pH 5.1, Microbatch, temperature 295K
Crystal grow
*PLUS
Temperature: 291 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120.4 mg/mlprotein1drop
21.6 Msodium citrate1reservoirpH5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 12, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. all: 40686 / Num. obs: 40654 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.4→1.45 Å / % possible all: 100
Reflection
*PLUS
Num. obs: 40686 / % possible obs: 99.8 % / Num. measured all: 286969 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 5.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B78

1b78


Resolution: 1.4→26.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1374304.66 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2038 5 %RANDOM
Rwork0.202 ---
obs0.202 40654 99.6 %-
all-40686 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.463 Å2 / ksol: 0.38057 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---5.58 Å20 Å2
3---4.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.4→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 13 202 1718
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellHighest resolution: 1.4 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork6361 -
Rfree-4.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMCIT.TOP
X-RAY DIFFRACTION3CIT.PARAM
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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