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- PDB-7aur: Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in co... -

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Basic information

Entry
Database: PDB / ID: 7aur
TitleYeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with AMP-PNP
ComponentsDiphosphoinositol 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 / endopolyphosphatase / diadenosine polyphosphate catabolic process / bis(5'-adenosyl)-hexaphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / endopolyphosphatase activity ...diadenosine hexaphosphate hydrolase (AMP-forming) / Synthesis of pyrophosphates in the cytosol / polyphosphate catabolic process / endopolyphosphatase / diadenosine polyphosphate catabolic process / bis(5'-adenosyl)-hexaphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / endopolyphosphatase activity / diphosphoinositol polyphosphate metabolic process / diphosphoinositol-polyphosphate diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / phosphodiesterase decapping endonuclease activity / diphosphoinositol-polyphosphate diphosphatase / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Diphosphoinositol polyphosphate phosphohydrolase DDP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4157
Polymers21,8131
Non-polymers1,6036
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-26 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.958, 61.958, 95.924
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-203-

ANP

21A-203-

ANP

31A-338-

HOH

41A-353-

HOH

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Components

#1: Protein 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: 21812.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GGS is a rest of purification linker, protein starts in MGK.
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.44 Å3/Da / Density % sol: 49.64 % / Description: Diamond-like
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 25% PEG 6000, 0.1 M Sodium acetate pH 5.0, 0.1 M NaCl. Protein:precipitant ratio 2:1. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM AMP-PNP.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2018 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→47.96 Å / Num. obs: 26240 / % possible obs: 99.8 % / Redundancy: 19 % / Biso Wilson estimate: 27.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.02 / Net I/σ(I): 18.9
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1299 / CC1/2: 0.937 / Rpim(I) all: 0.164 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AUI

7aui


Resolution: 1.65→46.87 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.173 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1336 5.1 %RANDOM
Rwork0.209 ---
obs0.2106 24867 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.48 Å2 / Biso mean: 35.977 Å2 / Biso min: 21.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å2-0 Å2
2--0.14 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 1.65→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 96 112 1366
Biso mean--66.67 45.4 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131300
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171164
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.6911781
X-RAY DIFFRACTIONr_angle_other_deg1.3011.6172724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7965146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57922.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72515223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.445159
X-RAY DIFFRACTIONr_chiral_restr0.0710.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 90 -
Rwork0.309 1816 -
all-1906 -
obs--99.84 %

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