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- PDB-6c45: Crystal structure of human inorganic pyrophosphatase in the P2121... -

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Basic information

Entry
Database: PDB / ID: 6c45
TitleCrystal structure of human inorganic pyrophosphatase in the P212121 space group
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / inorganic pyrophosphatase (PPase) family / hydrolysis of pyrophosphate to inorganic phosphate
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 / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inorganic pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.388 Å
AuthorsNiu, H. / Zhu, J. / Huang, X. / Du, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM116062-01 United States
CitationJournal: To be Published
Title: Expression, purification and crystallization of the human protein PPA1
Authors: Niu, H. / Zhu, J. / Huang, X. / Du, Z.
History
DepositionJan 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)130,8204
Polymers130,8204
Non-polymers00
Water9,476526
1
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)65,4102
Polymers65,4102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-16 kcal/mol
Surface area24600 Å2
MethodPISA
2
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)65,4102
Polymers65,4102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-14 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.250, 136.940, 216.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 (E. coli) / References: UniProt: Q15181, inorganic diphosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 100 mM Bis-Tris, pH 7.5, 200 mM potassium bromide, 10% v/v glycerol
PH range: 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0,987
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
101
29871
ReflectionResolution: 2.388→84.931 Å / Num. all: 60497 / Num. obs: 60497 / % possible obs: 99.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 39.18 Å2 / Rpim(I) all: 0.064 / Rrim(I) all: 0.136 / Rsym value: 0.119 / Net I/av σ(I): 4.8 / Net I/σ(I): 8.2 / Num. measured all: 269611
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.39-2.524.10.68713587386870.4010.8010.6872.299.5
2.52-2.674.60.4811.53756682340.2660.5520.4813.2100
2.67-2.854.60.3082.33524777440.1690.3530.3084.5100
2.85-3.084.60.2093.53319372600.1140.240.2096.3100
3.08-3.384.50.1444.63057067260.0760.1640.1449.1100
3.38-3.784.50.16.42755760930.0530.1140.111.8100
3.78-4.364.50.0768.12439954080.0390.0860.07614.2100
4.36-5.344.50.07972058946070.0410.0890.07915.499.9
5.34-7.554.40.06591596136290.0340.0740.06515.299.7
7.55-84.9314.10.0568.1865621090.0310.0650.05616.198.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALAdata scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.388→65.28 Å / FOM work R set: 0.8126 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.23 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 1998 3.31 %
Rwork0.193 58336 -
obs0.195 60334 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.39 Å2 / Biso mean: 25.02 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.388→65.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9031 0 0 526 9557
Biso mean---24.28 -
Num. residues----1135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089283
X-RAY DIFFRACTIONf_angle_d1.24812611
X-RAY DIFFRACTIONf_chiral_restr0.0841333
X-RAY DIFFRACTIONf_plane_restr0.0081647
X-RAY DIFFRACTIONf_dihedral_angle_d14.0933424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.388-2.44770.31411370.26814016415399
2.4477-2.51390.33951430.256541774320100
2.5139-2.58790.3141400.248640554195100
2.5879-2.67140.29971420.240841564298100
2.6714-2.76690.33071400.242640924232100
2.7669-2.87770.32621410.23741224263100
2.8777-3.00860.31311430.230841424285100
3.0086-3.16730.26991420.215841684310100
3.1673-3.36570.27561430.207841644307100
3.3657-3.62550.26381440.190741704314100
3.6255-3.99030.23561420.177241664308100
3.9903-4.56760.19831460.15142474393100
4.5676-5.75420.19121450.150342264371100
5.7542-65.30460.20981500.17284435458599

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