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- PDB-7cmo: Crystal structure of human inorganic pyrophosphatase -

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Basic information

Entry
Database: PDB / ID: 7cmo
TitleCrystal structure of human inorganic pyrophosphatase
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 / cytosol / cytoplasm
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: 3.4 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
DepositionJul 28, 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

Downloads & links

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)130,8204
Polymers130,8204
Non-polymers00
Water0
1
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)65,4102
Polymers65,4102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-13 kcal/mol
Surface area24330 Å2
MethodPISA
2
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)65,4102
Polymers65,4102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-14 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.905, 135.041, 212.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))
21(chain B and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))
31(chain C and resid 24 through 306)
41(chain D and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))A24 - 44
121(chain A and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))A46 - 124
131(chain A and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))A133 - 306
211(chain B and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))B24 - 44
221(chain B and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))B46 - 124
231(chain B and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))B133 - 306
311(chain C and resid 24 through 306)C24 - 306
411(chain D and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))D24 - 44
421(chain D and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))D46 - 124
431(chain D and (resid 24 through 44 or resid 46 through 124 or resid 133 through 306))D133 - 306

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Components

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


Mass: 32705.037 Da / Num. of mol.: 4
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
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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20%PEG4K, 50mM Li2SO4,50 Mm Na2SO4,pH 5.5

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.597→48.97 Å / Num. obs: 20300 / % possible obs: 97.5 % / Redundancy: 3.05 % / CC1/2: 0.998 / Net I/σ(I): 7.7
Reflection shellResolution: 3.4→3.521 Å / Num. unique obs: 20287 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C45

6c45


Resolution: 3.4→39.06 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 1013 4.99 %
Rwork0.2206 19274 -
obs0.2234 20287 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.84 Å2 / Biso mean: 105.8269 Å2 / Biso min: 73.45 Å2
Refinement stepCycle: final / Resolution: 3.4→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8919 0 0 0 8919
Num. residues----1120
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3285X-RAY DIFFRACTION9.426TORSIONAL
12B3285X-RAY DIFFRACTION9.426TORSIONAL
13C3285X-RAY DIFFRACTION9.426TORSIONAL
14D3285X-RAY DIFFRACTION9.426TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.580.3581440.31332743288799
3.58-3.80.32281380.29432628276696
3.8-4.10.31871450.275327392884100
4.1-4.510.30391460.21427772923100
4.51-5.160.24971440.19062743288799
5.16-6.50.28581470.20862790293798
6.5-39.060.23271490.19212854300396
Refinement TLS params.Method: refined / Origin x: 6.0387 Å / Origin y: -1.2126 Å / Origin z: -39.0941 Å
111213212223313233
T0.8961 Å20.0184 Å20.0776 Å2-1.0049 Å20.045 Å2--0.9895 Å2
L0.1216 °2-0.1389 °20.3829 °2-0.2861 °20.0993 °2--0.6569 °2
S-0.0894 Å °-0.0074 Å °0.058 Å °0.1149 Å °-0.0453 Å °0.016 Å °0.0837 Å °0.1311 Å °0.136 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 288
2X-RAY DIFFRACTION1allB3 - 286
3X-RAY DIFFRACTION1allC3 - 287
4X-RAY DIFFRACTION1allD4 - 286

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