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- PDB-8qpt: Crystal structure of pyrophosphatase from Ogataea parapolymorpha -

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Basic information

Entry
Database: PDB / ID: 8qpt
TitleCrystal structure of pyrophosphatase from Ogataea parapolymorpha
Componentsinorganic diphosphatase
KeywordsHYDROLASE / pyrophosphatase / holo-form
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / nucleus / cytoplasm
Similarity search - Function
Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase
Similarity search - Domain/homology
inorganic diphosphatase
Similarity search - Component
Biological speciesOgataea parapolymorpha (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatyuta, I.O. / Rodina, E.V. / Vorobyeva, N.N. / Kurilova, S.A. / Bezpalaya, E.Y. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-24-00177 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: The crystal structure of yeast mitochondrial type pyrophosphatase provides a model to study pathological mutations in its human ortholog.
Authors: Bezpalaya, E.Y. / Matyuta, I.O. / Vorobyeva, N.N. / Kurilova, S.A. / Oreshkov, S.D. / Minyaev, M.E. / Boyko, K.M. / Rodina, E.V.
History
DepositionOct 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: inorganic diphosphatase
B: inorganic diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6198
Polymers65,3382
Non-polymers2816
Water7,422412
1
A: inorganic diphosphatase
hetero molecules

B: inorganic diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6198
Polymers65,3382
Non-polymers2816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2850 Å2
ΔGint-51 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.724, 83.035, 64.975
Angle α, β, γ (deg.)90.00, 96.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein inorganic diphosphatase


Mass: 32669.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ogataea parapolymorpha (fungus) / Gene: HPODL_03436 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W1QGT4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 9% P6K, 0.1M Tris pH 8.6, 0.1 M natrium formiat

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→21 Å / Num. obs: 55406 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Χ2: 0.96 / Net I/σ(I): 18.9 / Num. measured all: 365344
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.836 / Num. measured all: 21629 / Num. unique obs: 3268 / CC1/2: 0.831 / Rpim(I) all: 0.35 / Rrim(I) all: 0.908 / Χ2: 0.98 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.993 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21215 2708 4.9 %RANDOM
Rwork0.17032 ---
obs0.1724 52651 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å2-1.52 Å2
2--0.88 Å20 Å2
3----0.9 Å2
Refinement stepCycle: 1 / Resolution: 1.8→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4425 0 16 412 4853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0134593
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164230
X-RAY DIFFRACTIONr_angle_refined_deg2.081.646239
X-RAY DIFFRACTIONr_angle_other_deg1.5181.5789757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2235578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27624.605215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20815721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8281513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025223
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02987
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4142.3872294
X-RAY DIFFRACTIONr_mcbond_other3.412.3862293
X-RAY DIFFRACTIONr_mcangle_it4.6563.5692866
X-RAY DIFFRACTIONr_mcangle_other4.6563.5692867
X-RAY DIFFRACTIONr_scbond_it4.1462.6052299
X-RAY DIFFRACTIONr_scbond_other4.1232.612284
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8463.783370
X-RAY DIFFRACTIONr_long_range_B_refined7.12728.0645129
X-RAY DIFFRACTIONr_long_range_B_other7.05327.7685044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8670 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 199 -
Rwork0.257 3834 -
obs--99.85 %

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