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- PDB-2duk: Crystal structure of MS0616 -

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Basic information

Entry
Database: PDB / ID: 2duk
TitleCrystal structure of MS0616
ComponentsMS0616
KeywordsHYDROLASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Synthesis of pyrophosphates in the cytosol / inositol diphosphate pentakisphosphate diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / diphosphoinositol polyphosphate metabolic process / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diphosphoinositol-polyphosphate diphosphatase ...Synthesis of pyrophosphates in the cytosol / inositol diphosphate pentakisphosphate diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase 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 / bis(5'-adenosyl)-pentaphosphatase activity / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleus / metal ion binding / cytoplasm / cytosol
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
Diphosphoinositol polyphosphate phosphohydrolase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsHosaka, T. / Nishino, A. / Uchikubo, K.-T. / Kishishita, S. / Murayama, K. / Shirouzu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of MS0616
Authors: Hosaka, T. / Nishino, A. / Uchikubo, K.-T. / Kishishita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionJul 24, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: MS0616
B: MS0616


Theoretical massNumber of molelcules
Total (without water)31,9402
Polymers31,9402
Non-polymers00
Water1,09961
1
A: MS0616


Theoretical massNumber of molelcules
Total (without water)15,9701
Polymers15,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MS0616


Theoretical massNumber of molelcules
Total (without water)15,9701
Polymers15,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.891, 41.448, 189.288
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 MS0616 / Diphosphoinositol polyphosphate phosphohydrolase 2 / DIPP-2 / Diadenosine 5' / 5'''-P1 / P6- ...Diphosphoinositol polyphosphate phosphohydrolase 2 / DIPP-2 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 2 / Nucleoside diphosphate-linked moiety X motif 4 / Nudix motif 4


Mass: 15970.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Plasmid: PX051128-08
References: UniProt: Q8R2U6, diphosphoinositol-polyphosphate diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0M Ammonium Sulphate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 7, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 9612 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 4.33854 % / Rmerge(I) obs: 0.181 / Rsym value: 0.114 / Net I/σ(I): 8.46597
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.44845 / Num. unique all: 483 / Rsym value: 0.293 / % possible all: 66.62

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FVV

2fvv


Resolution: 2.62→45 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.88 / SU B: 14.732 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 3.472 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28747 455 4.7 %RANDOM
Rwork0.24676 ---
obs0.24871 9145 93.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.176 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---2.24 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.62→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 0 61 2261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222246
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9663022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91923.391115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.08415414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9921522
X-RAY DIFFRACTIONr_chiral_restr0.1170.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021710
X-RAY DIFFRACTIONr_nbd_refined0.2680.21060
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21462
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.27
X-RAY DIFFRACTIONr_mcbond_it0.8431.51379
X-RAY DIFFRACTIONr_mcangle_it1.46322139
X-RAY DIFFRACTIONr_scbond_it1.73331006
X-RAY DIFFRACTIONr_scangle_it2.834.5883
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 35 -
Rwork0.379 448 -
obs--66.62 %

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