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- PDB-2fvv: Human Diphosphoinositol polyphosphate phosphohydrolase 1 -

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Basic information

Entry
Database: PDB / ID: 2fvv
TitleHuman Diphosphoinositol polyphosphate phosphohydrolase 1
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / diphosphoinositol polyphosphate phosphohydrolase / NUDIX / inositol polyphosphate metabolism / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


diphosphoinositol polyphosphate catabolic process / inositol diphosphate pentakisphosphate diphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity ...diphosphoinositol polyphosphate catabolic process / inositol diphosphate pentakisphosphate diphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / diphosphoinositol polyphosphate metabolic process / RNA decapping / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diphosphoinositol-polyphosphate diphosphatase / diphosphoinositol-polyphosphate diphosphatase activity / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / diadenosine hexaphosphate hydrolase (ATP-forming) / Synthesis of pyrophosphates in the cytosol / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cell-cell signaling / manganese ion binding / magnesium ion binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsHallberg, B.M. / Kursula, P. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. ...Hallberg, B.M. / Kursula, P. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hogbom, M. / Holmberg-Schiavone, L. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / van den Berg, S. / Weigelt, J. / Persson, C. / Structural Genomics Consortium (SGC)
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of human diphosphoinositol phosphatase 1
Authors: Thorsell, A.G. / Persson, C. / Graslund, S. / Hammarstrom, M. / Busam, R.D. / Hallberg, B.M.
History
DepositionJan 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Apr 3, 2019Group: Advisory / Atomic model / Data collection
Category: atom_site / atom_site_anisotrop / pdbx_distant_solvent_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3]
Revision 2.1Oct 14, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details ..._chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Mar 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: Diphosphoinositol polyphosphate phosphohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8474
Polymers22,0561
Non-polymers7923
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.653, 59.900, 61.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diphosphoinositol polyphosphate phosphohydrolase 1 / DIPP-1 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 1 / Nucleoside diphosphate-linked ...DIPP-1 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 1 / Nucleoside diphosphate-linked moiety X motif 3 / Nudix motif 3


Mass: 22055.725 Da / Num. of mol.: 1 / Fragment: residues 8-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT3, DIPP, DIPP1 / Plasmid: pNIC-BSA4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3)
References: UniProt: O95989, diphosphoinositol-polyphosphate diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG8000, 0.2M Lithium sulphate, 0.1M SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODEBRUKER AXS MICROSTAR11.54181.5418
SYNCHROTRONMAX II I911-520.979570.97957
Detector
TypeIDDetectorDateDetails
Bruker Platinum 1351CCDDec 27, 2005Helios Multilayer
MARRESEARCH2CCDDec 14, 2005Double crystal monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Helios multilayerSINGLE WAVELENGTHMx-ray1
2Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.979571
ReflectionResolution: 1.25→27.44 Å / Num. all: 50655 / Num. obs: 45852 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.88 % / Rmerge(I) obs: 0.0809 / Net I/σ(I): 23.93
Reflection shellResolution: 1.25→1.34 Å / Redundancy: 1.55 % / Rmerge(I) obs: 0.2757 / Mean I/σ(I) obs: 2.74 / % possible all: 58.1

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT1.701data extraction
PROTEUM PLUSdata reduction
SAINTdata reduction
XDSdata reduction
SADABSdata scaling
XSCALEdata scaling
SHELXDphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.25→10 Å / Num. parameters: 12858 / Num. restraintsaints: 16308 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.6%
RfactorNum. reflection% reflectionSelection details
Rfree0.222 922 1.1 %RANDOM
Rwork0.171 ---
all0.173 50655 --
obs0.171 45852 90.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 25.492 Å2
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 42 192 1415
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.109
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.071
X-RAY DIFFRACTIONs_approx_iso_adps0.122

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