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

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Basic information

Entry
Database: PDB / ID: 7aum
TitleYeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with 5-PCF2Am-InsP5
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
Chem-KDJ / Diphosphoinositol polyphosphate phosphohydrolase DDP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.07 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)22,5502
Polymers21,8131
Non-polymers7371
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.809, 61.809, 95.474
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-324-

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-KDJ / (1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic acid


Mass: 737.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19F2NO24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.42 Å3/Da / Density % sol: 49.16 % / Description: Bypiramid
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 27% PEG 3350, 0.1 M Sodium acetate pH 4.5, 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 5-PCF2Am-InsP5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 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: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.07→47.74 Å / Num. obs: 13380 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 40.539 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.018 / Net I/σ(I): 23.3
Reflection shellResolution: 2.07→2.13 Å / Redundancy: 19.8 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1025 / CC1/2: 0.945 / Rpim(I) all: 0.156 / % 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: 2.07→46.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.95 / SU B: 14.57 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 670 5 %RANDOM
Rwork0.224 ---
obs0.2247 12678 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 179.36 Å2 / Biso mean: 67.143 Å2 / Biso min: 37.88 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.07→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 41 33 1433
Biso mean--133.93 55.7 -
Num. residues----167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131441
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171352
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.6761958
X-RAY DIFFRACTIONr_angle_other_deg1.1541.5913137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23521.97581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85515267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1371512
X-RAY DIFFRACTIONr_chiral_restr0.0530.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
LS refinement shellResolution: 2.07→2.124 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 52 -
Rwork0.328 912 -
all-964 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 14.197 Å / Origin y: -21.7035 Å / Origin z: -2.2294 Å
111213212223313233
T0.5322 Å2-0.3024 Å20.0291 Å2-0.2382 Å2-0.0056 Å2--0.133 Å2
L1.8803 °20.6465 °20.6545 °2-1.2372 °2-0.3895 °2--1.137 °2
S0.4264 Å °-0.1338 Å °0.1335 Å °0.4698 Å °-0.3413 Å °0.079 Å °0.1818 Å °-0.1239 Å °-0.0851 Å °

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