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- PDB-2q9p: Human diphosphoinositol polyphosphate phosphohydrolase 1, Mg-F complex -

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Basic information

Entry
Database: PDB / ID: 2q9p
TitleHuman diphosphoinositol polyphosphate phosphohydrolase 1, Mg-F complex
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE / NUDIX / INOSITOL PYROPHOSPHATE METABOLISM / 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 / 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 / bis(5'-adenosyl)-pentaphosphatase activity / 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
FLUORIDE ION / INOSITOL HEXAKISPHOSPHATE / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsThorsell, A.G. / Busam, R. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. ...Thorsell, A.G. / Busam, R. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nordlund, P. / Nyman, T. / Ogg, D. / Sagemark, J. / Sundstrom, M. / Van den Berg, S. / Weigelt, J. / Welin, M. / Persson, C. / Hallberg, B.M. / 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
DepositionJun 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 14, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_dist_value ..._chem_comp.pdbx_synonyms / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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: Diphosphoinositol polyphosphate phosphohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,03817
Polymers22,0561
Non-polymers98316
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.193, 59.444, 62.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Uterus / 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

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Non-polymers , 5 types, 162 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: F
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG 8000, 200 mM LiCl, 5 mM MgCl2, 20 mM NaF, 5 mM IP6, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 19, 2007 / Details: Helios multilayer mirrors
RadiationMonochromator: Helios multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 20890 / Num. obs: 20848 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rsym value: 0.054 / Net I/σ(I): 11.7
Reflection shellResolution: 1.65→1.75 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.461 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
PROTEUM PLUS2data collection
SAINTdata reduction
SADABSdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2FVV

2fvv


Resolution: 1.65→32.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.277 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Structure was determined starting from rigid body refinement of the PDB entry 2FVV with Refmac 5 program. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1067 5.1 %RANDOM
Rwork0.192 ---
all0.194 20848 --
obs0.194 20813 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 87 146 1343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211210
X-RAY DIFFRACTIONr_bond_other_d0.0020.02819
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9091661
X-RAY DIFFRACTIONr_angle_other_deg1.0012.991960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11223.44361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8115204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6311512
X-RAY DIFFRACTIONr_chiral_restr0.1220.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021294
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02247
X-RAY DIFFRACTIONr_nbd_refined0.2120.2270
X-RAY DIFFRACTIONr_nbd_other0.2150.2891
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2567
X-RAY DIFFRACTIONr_nbtor_other0.0940.2649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1880.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.213
X-RAY DIFFRACTIONr_mcbond_it1.5911.5873
X-RAY DIFFRACTIONr_mcbond_other0.3571.5276
X-RAY DIFFRACTIONr_mcangle_it1.76121100
X-RAY DIFFRACTIONr_scbond_it3.2113615
X-RAY DIFFRACTIONr_scangle_it4.4694.5561
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 84 -
Rwork0.32 1404 -
obs-1488 98.22 %

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