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- PDB-3mcf: Crystal structure of human diphosphoinositol polyphosphate phosph... -

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Basic information

Entry
Database: PDB / ID: 3mcf
TitleCrystal structure of human diphosphoinositol polyphosphate phosphohydrolase 3-alpha
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 3-alpha
KeywordsHYDROLASE / DIPP3A / NUDT10 / APS2 / NUDIX / diphosphoinositol pentakisphosphate / SIGNAL TRANSDUCTION / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / SGC STOCKHOLM / Metal-binding
Function / homology
Function and homology information


: / diadenosine hexaphosphate hydrolase (AMP-forming) / inositol diphosphate pentakisphosphate diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / diphosphoinositol polyphosphate metabolic process / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process ...: / diadenosine hexaphosphate hydrolase (AMP-forming) / inositol diphosphate pentakisphosphate diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / diphosphoinositol polyphosphate metabolic process / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diphosphoinositol-polyphosphate diphosphatase / diphosphoinositol-polyphosphate diphosphatase activity / Synthesis of pyrophosphates in the cytosol / inositol phosphate metabolic process / metal 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
CITRATE ANION / Diphosphoinositol polyphosphate phosphohydrolase 3-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 3-alpha
Authors: Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / ...Authors: Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Wisniewska, M. / Nordlund, P.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diphosphoinositol polyphosphate phosphohydrolase 3-alpha
B: Diphosphoinositol polyphosphate phosphohydrolase 3-alpha
A: CITRATE ANION
B: CITRATE ANION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0465
Polymers31,5762
Non-polymers4703
Water3,981221
1
A: Diphosphoinositol polyphosphate phosphohydrolase 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9772
Polymers15,7881
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diphosphoinositol polyphosphate phosphohydrolase 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0693
Polymers15,7881
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.390, 79.549, 88.729
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 3-alpha / DIPP-3-alpha / DIPP3-alpha / hDIPP3alpha / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 3- ...DIPP-3-alpha / DIPP3-alpha / hDIPP3alpha / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 3-alpha / Nucleoside diphosphate-linked moiety X motif 10 / Nudix motif 10 / hAps2


Mass: 15787.897 Da / Num. of mol.: 2 / Fragment: UNP residues 17 to 144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APS2, DIPP3A, NUDT10 / Plasmid: pNIC-CH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 R3 pRARE
References: UniProt: Q8NFP7, diphosphoinositol-polyphosphate diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 19.8% PEG3000, 0.01M sodium acetate trihydrate pH 4.6, 0.1M tri-sodium citrate dihydrate pH 5.5, 0.12M tri-sodium citrate dihydrate unbuffered, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 26, 2009 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→32.5 Å / Num. all: 27630 / Num. obs: 27499 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 19.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 5.1 / Num. unique all: 25993 / Rsym value: 0.444 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DUK

2duk


Resolution: 2→32.503 Å / SU ML: 0.25 / Isotropic thermal model: ISOTROPIC / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1373 5 %RANDOM
Rwork0.1732 ---
obs0.1754 27450 99.35 %-
all-27630 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.948 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 28.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.5423 Å21.7306 Å2-1.1883 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→32.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 32 221 2321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052148
X-RAY DIFFRACTIONf_angle_d0.9462903
X-RAY DIFFRACTIONf_dihedral_angle_d16.207829
X-RAY DIFFRACTIONf_chiral_restr0.067303
X-RAY DIFFRACTIONf_plane_restr0.004375
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0001-2.07160.30131280.21122435256394
2.0716-2.15450.28291360.185425752711100
2.1545-2.25260.20741360.179325762712100
2.2526-2.37130.25491350.162925632698100
2.3713-2.51980.21181380.184726212759100
2.5198-2.71430.24321360.184926012737100
2.7143-2.98720.22861380.176526182756100
2.9872-3.41910.19191380.156526312769100
3.4191-4.30610.18471410.138826632804100
4.3061-32.5070.18671470.17327942941100

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