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- PDB-7auu: Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1-nose ... -

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Basic information

Entry
Database: PDB / ID: 7auu
TitleYeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1-nose mutant in complex with InsP6
ComponentsDiphosphoinositol polyphosphate phosphohydrolase DDP1,Diphosphoinositol polyphosphate phosphohydrolase DDP1
KeywordsHYDROLASE / Inositol / PP-InsP / Pyrophosphatase / Polyphosphate / Diadenosine polyphosphate / DDP1 / Nudix
Function / homology
Function and homology information


diadenosine hexaphosphate hydrolase (AMP-forming) / Synthesis of pyrophosphates in the cytosol / polyphosphate catabolic process / phosphodiesterase decapping endonuclease activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / diphosphoinositol polyphosphate metabolic process ...diadenosine hexaphosphate hydrolase (AMP-forming) / Synthesis of pyrophosphates in the cytosol / polyphosphate catabolic process / phosphodiesterase decapping endonuclease activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 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 / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Diphosphoinositol polyphosphate phosphohydrolase DDP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsMarquez-Monino, M.A. / Gonzalez, B.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2017-89913-P Spain
CitationJournal: Sci Adv / Year: 2021
Title: Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping.
Authors: Marquez-Monino, M.A. / Ortega-Garcia, R. / Shipton, M.L. / Franco-Echevarria, E. / Riley, A.M. / Sanz-Aparicio, J. / Potter, B.V.L. / Gonzalez, B.
History
DepositionNov 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 DDP1,Diphosphoinositol polyphosphate phosphohydrolase DDP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8793
Polymers19,1951
Non-polymers6842
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-16 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.120, 62.120, 92.472
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Diphosphoinositol polyphosphate phosphohydrolase DDP1,Diphosphoinositol polyphosphate phosphohydrolase DDP1 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase / Ap6A hydrolase / Diadenosine and ...Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase / Ap6A hydrolase / Diadenosine and diphosphoinositol polyphosphate phosphohydrolase 1 / Diadenosine hexaphosphate hydrolase (AMP-forming)


Mass: 19194.779 Da / Num. of mol.: 1 / Mutation: Deletion 104-126
Source method: isolated from a genetically manipulated source
Details: GGS is a rest of purification linker, protein starts in MGK. This protein has a deletion in P104-H126, where it has been replaced by GGG.,GGS is a rest of purification linker, protein starts ...Details: GGS is a rest of purification linker, protein starts in MGK. This protein has a deletion in P104-H126, where it has been replaced by GGG.,GGS is a rest of purification linker, protein starts in MGK. This protein has a deletion in P104-H126, where it has been replaced by GGG.,GGS is a rest of purification linker, protein starts in MGK. This protein has a deletion in P104-H126, where it has been replaced by GGG.,GGS is a rest of purification linker, protein starts in MGK. This protein has a deletion in P104-H126, where it has been replaced by GGG.
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: DDP1, YOR163W, O3575 / Plasmid: pKLSLt / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta2(DE3)
References: UniProt: Q99321, diphosphoinositol-polyphosphate diphosphatase, diadenosine hexaphosphate hydrolase (AMP-forming)
#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.1 M Bis-Tris propane pH 6.5, 0.2 M Sodium nitrate. Protein:precipitant ratio 3:1. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM InsP6.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 2.45→46.54 Å / Num. obs: 7984 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 69.364 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.016 / Net I/σ(I): 21.3
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 873 / CC1/2: 0.937 / Rpim(I) all: 0.178 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7AUI

7aui


Resolution: 2.45→46.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 27.717 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 422 5.3 %RANDOM
Rwork0.2057 ---
obs0.2081 7535 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167.47 Å2 / Biso mean: 88.619 Å2 / Biso min: 49.21 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å2-1.42 Å2-0 Å2
2---2.84 Å20 Å2
3---9.2 Å2
Refinement stepCycle: final / Resolution: 2.45→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 37 15 1198
Biso mean--126.5 69.13 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131206
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171137
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.6751640
X-RAY DIFFRACTIONr_angle_other_deg1.0871.5842637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.83321.93562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19815216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.509159
X-RAY DIFFRACTIONr_chiral_restr0.0470.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
LS refinement shellResolution: 2.451→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 31 -
Rwork0.327 532 -
all-563 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.4514 Å / Origin y: -19.8554 Å / Origin z: -1.6939 Å
111213212223313233
T0.3094 Å2-0.1434 Å20.002 Å2-0.3169 Å2-0.0044 Å2--0.0657 Å2
L2.8968 °21.345 °21.0999 °2-2.1131 °2-0.1887 °2--1.0304 °2
S0.1036 Å °-0.132 Å °-0.1578 Å °0.1938 Å °-0.1968 Å °-0.3493 Å °0.0144 Å °-0.2672 Å °0.0932 Å °

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