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- PDB-8j7q: The active site mutant of human inorganic pyrophosphatase -

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Basic information

Entry
Database: PDB / ID: 8j7q
TitleThe active site mutant of human inorganic pyrophosphatase
ComponentsInorganic pyrophosphatase
KeywordsSTRUCTURAL PROTEIN / human inorganic pyrophosphatase
Function / homology
Function and homology information


Pyrophosphate hydrolysis / inorganic diphosphatase / Cytosolic tRNA aminoacylation / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase
Similarity search - Domain/homology
Inorganic pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHu, F. / Zheng, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The active site mutant of human inorganic pyrophosphatase
Authors: Hu, F. / Zheng, S.
History
DepositionApr 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)32,5471
Polymers32,5471
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Inorganic pyrophosphatase

A: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)65,0942
Polymers65,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2020 Å2
ΔGint-15 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.354, 90.765, 94.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase


Mass: 32546.971 Da / Num. of mol.: 1 / Mutation: D116A/D118A/P119A/D121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPA1, IOPPP, PP / Production host: Escherichia coli (E. coli) / References: UniProt: Q15181, inorganic diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.2 M (NH4)2SO4, 20% PEG8000, 100 mM MES PH6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.69→19.08 Å / Num. obs: 39785 / % possible obs: 95.31 % / Redundancy: 12.5 % / CC1/2: 0.999 / Net I/σ(I): 11.97
Reflection shellResolution: 1.69→1.752 Å / Num. unique obs: 2248 / CC1/2: 0.0176

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→19.08 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 36.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1978 5.12 %
Rwork0.2155 --
obs0.217 38612 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 0 196 2249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d5.908273
X-RAY DIFFRACTIONf_chiral_restr0.058308
X-RAY DIFFRACTIONf_plane_restr0.008366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.4429600.52551158X-RAY DIFFRACTION43
1.73-1.780.50271290.52532594X-RAY DIFFRACTION96
1.78-1.830.51051630.46332680X-RAY DIFFRACTION99
1.83-1.890.48261310.46352712X-RAY DIFFRACTION100
1.89-1.960.39671530.39662679X-RAY DIFFRACTION99
1.96-2.040.31781410.3092719X-RAY DIFFRACTION100
2.04-2.130.27571610.28632710X-RAY DIFFRACTION100
2.13-2.240.28461390.24112711X-RAY DIFFRACTION100
2.24-2.380.28761530.24992737X-RAY DIFFRACTION100
2.38-2.570.30351490.2252754X-RAY DIFFRACTION100
2.57-2.830.25451480.21492735X-RAY DIFFRACTION100
2.83-3.230.25121540.20312768X-RAY DIFFRACTION100
3.23-4.070.20371450.17882788X-RAY DIFFRACTION100
4.07-19.080.18741520.17272889X-RAY DIFFRACTION100

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