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- PDB-7btn: Crystal structure of human inorganic pyrophosphatase with metal ions -

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Basic information

Entry
Database: PDB / ID: 7btn
TitleCrystal structure of human inorganic pyrophosphatase with metal ions
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / Complex / Monomer
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: 2.382 Å
AuthorsHu, F. / Huang, Z. / Li, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81802001 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural and biochemical characterization of inorganic pyrophosphatase from Homo sapiens.
Authors: Hu, F. / Huang, Z. / Zheng, S. / Wu, Q. / Chen, Y. / Lin, H. / Huang, W. / Li, L.
History
DepositionApr 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: 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: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1593
Polymers35,1111
Non-polymers492
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.406, 89.517, 95.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 35110.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPA1, IOPPP, PP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15181, inorganic diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG4000, 50mM magnesium acetate, pH 5.5

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.382→19.771 Å / Num. obs: 14729 / % possible obs: 99.6005 % / Redundancy: 1.71 % / CC1/2: 0.998 / Net I/σ(I): 1.71
Reflection shellResolution: 2.382→2.467 Å / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
xia2data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M38

1m38


Resolution: 2.382→19.771 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.09
RfactorNum. reflection% reflection
Rfree0.2104 731 4.97 %
Rwork0.1787 --
obs0.1803 14707 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.12 Å2 / Biso mean: 39.8589 Å2 / Biso min: 19.27 Å2
Refinement stepCycle: final / Resolution: 2.382→19.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 2 76 2275
Biso mean--30 38.28 -
Num. residues----275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3825-2.56610.29951420.1959276499
2.5661-2.82360.26511370.20222751100
2.8236-3.23070.21691350.19942795100
3.2307-4.06450.19071640.17022774100
4.0645-19.7710.18941530.1642893100

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