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- PDB-2dvn: Structure of PH1917 protein with the complex of IMP from Pyrococc... -

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Basic information

Entry
Database: PDB / ID: 2dvn
TitleStructure of PH1917 protein with the complex of IMP from Pyrococcus horikoshii
ComponentsHypothetical protein PH1917
KeywordsHYDROLASE / IMP / NTPase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / 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
INOSINIC ACID / dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLokanath, N.K. / 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
DepositionJul 31, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 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
B: Hypothetical protein PH1917
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,68820
Polymers42,4672
Non-polymers2,22218
Water7,656425
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.295, 80.295, 162.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1667-

HOH

21A-1668-

HOH

31A-1671-

HOH

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Components

#1: Protein Hypothetical protein PH1917 / NTPase


Mass: 21233.420 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: O59580
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 425 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6
Details: Ammonium phosphate, Sodium acetate, pH 4.6, microbatch, 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: Feb 28, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 70260 / Num. obs: 70170 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.1
Reflection shellResolution: 1.6→1.66 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V7R

1v7r


Resolution: 1.6→39.18 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2224547 / 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
Rfree0.188 3577 5.1 %RANDOM
Rwork0.183 ---
obs0.183 70170 99.2 %-
all-70260 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5845 Å2 / ksol: 0.403357 e/Å3
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2---0.91 Å20 Å2
3---1.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.6→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 129 425 3560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it0.961.5
X-RAY DIFFRACTIONc_mcangle_it1.52
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.202 596 5.3 %
Rwork0.193 10618 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4lig.paramlig.top

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