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- PDB-5ls0: Crystal structure of Inorganic Pyrophosphatase PPA1 from Arabidop... -

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Basic information

Entry
Database: PDB / ID: 5ls0
TitleCrystal structure of Inorganic Pyrophosphatase PPA1 from Arabidopsis thaliana
ComponentsSoluble inorganic pyrophosphatase 1
KeywordsHYDROLASE / inorganic pyrophosphatase / OB-fold
Function / homology
Function and homology information


regulation of starch metabolic process / sucrose metabolic process / cell wall biogenesis / inorganic diphosphatase / inorganic diphosphate phosphatase activity / lipid storage / phosphate-containing compound metabolic process / magnesium ion binding / nucleoplasm / nucleus ...regulation of starch metabolic process / sucrose metabolic process / cell wall biogenesis / inorganic diphosphatase / inorganic diphosphate phosphatase activity / lipid storage / phosphate-containing compound metabolic process / magnesium ion binding / nucleoplasm / nucleus / 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
DI(HYDROXYETHYL)ETHER / Soluble inorganic pyrophosphatase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsGrzechowiak, M. / Sikorski, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Poland
Citation
Journal: Biochem.J. / Year: 2019
Title: Crystal structures of plant inorganic pyrophosphatase, an enzyme with a moonlighting autoproteolytic activity.
Authors: Grzechowiak, M. / Ruszkowski, M. / Sliwiak, J. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M.
#1: Journal: Plant Science / Year: 2007
Title: Characterization of two soluble inorganic pyrophosphatases from Arabidopsis thaliana
Authors: Navarro-De la Sancha, E. / Coello-Coutino, M. / Valencia-Turcotte, L.G. / Hernandez-Dominguez, E.E. / Trejo-Yepes, G. / Rodriguez-Sotres, R.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005
Title: Structure of inorganic pyrophosphatase from Helicobacter pylori.
Authors: Wu, C.A. / Lokanath, N.K. / Kim, D.Y. / Park, H.J. / Hwang, H.Y. / Kim, S.T. / Suh, S.W. / Kim, K.K.
#3: Journal: Biochemistry / Year: 2007
Title: A complete structural description of the catalytic cycle of yeast pyrophosphatase.
Authors: Oksanen, E. / Ahonen, A.K. / Tuominen, H. / Tuominen, V. / Lahti, R. / Goldman, A. / Heikinheimo, P.
#4: Journal: J. Mol. Biol. / Year: 2007
Title: Reversible inhibition of Escherichia coli inorganic pyrophosphatase by fluoride: trapped catalytic intermediates in cryo-crystallographic studies.
Authors: Samygina, V.R. / Moiseev, V.M. / Rodina, E.V. / Vorobyeva, N.N. / Popov, A.N. / Kurilova, S.A. / Nazarova, T.I. / Avaeva, S.M. / Bartunik, H.D.
History
DepositionAug 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble inorganic pyrophosphatase 1
B: Soluble inorganic pyrophosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3006
Polymers41,0392
Non-polymers2614
Water3,351186
1
A: Soluble inorganic pyrophosphatase 1
hetero molecules

A: Soluble inorganic pyrophosphatase 1
hetero molecules

A: Soluble inorganic pyrophosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6316
Polymers61,5583
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5100 Å2
ΔGint-57 kcal/mol
Surface area22400 Å2
MethodPISA
2
B: Soluble inorganic pyrophosphatase 1
hetero molecules

B: Soluble inorganic pyrophosphatase 1
hetero molecules

B: Soluble inorganic pyrophosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,26812
Polymers61,5583
Non-polymers7109
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5960 Å2
ΔGint-61 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.130, 81.130, 174.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-511-

HOH

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Components

#1: Protein Soluble inorganic pyrophosphatase 1 / Pyrophosphate phospho-hydrolase 1 / PPase 1


Mass: 20519.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PPA1, At1g01050, T25K16.5 / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93V56, inorganic diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg / References: inorganic diphosphatase
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.07 M bicine, 7% (w/v) PEG 6000, pH 9.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91814 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 28, 2013
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI -111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91814 Å / Relative weight: 1
ReflectionResolution: 1.79→40.564 Å / Num. obs: 40001 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 30.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/av σ(I): 21.9 / Net I/σ(I): 21.92
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.79-1.96.31.0871.90.751199
1.9-2.030.5373.80.919199.7
2.03-2.20.2647.50.978199.8
2.2-2.410.14213.330.993199.9
2.41-2.690.09419.350.996199.9
2.69-3.10.0532.730.999199.9
3.1-3.790.0353.310.9991100
3.79-5.340.02272.661199.9
5.34-40.5640.01977.091199.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lug

4lug


Resolution: 1.83→19.407 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 22.71
RfactorNum. reflection% reflection
Rfree0.1903 1000 2.65 %
Rwork0.1538 --
obs0.1548 37724 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.66 Å2 / Biso mean: 43.5848 Å2 / Biso min: 18.02 Å2
Refinement stepCycle: final / Resolution: 1.83→19.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 16 187 3061
Biso mean--68.37 41.24 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112941
X-RAY DIFFRACTIONf_angle_d1.2643988
X-RAY DIFFRACTIONf_chiral_restr0.055437
X-RAY DIFFRACTIONf_plane_restr0.008517
X-RAY DIFFRACTIONf_dihedral_angle_d13.9541122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8301-1.92650.3291430.294952465389
1.9265-2.04710.23711420.208352135355
2.0471-2.2050.20341430.173752615404
2.205-2.42650.18871420.159352395381
2.4265-2.77670.21361430.165852575400
2.7767-3.4950.19631430.157452515394
3.495-19.40770.16041440.124552575401
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.23180.32110.32551.68690.54431.39570.0730.2254-0.0062-0.4145-0.02270.2165-0.1704-0.4104-0.06250.29840.0168-0.05990.35710.02230.255329.183524.8392143.1357
21.35140.10820.18291.88741.2022.53250.13050.1081-0.0574-0.2427-0.1180.434-0.0857-0.6671-0.07510.2774-0.0098-0.07730.45470.02530.347921.796121.2262150.0919
32.74621.7054-1.46577.5117-2.69854.95660.2796-0.18240.09960.0128-0.05130.3864-0.2343-0.9481-0.17090.26220.048-0.03520.53550.02670.368116.781326.6346160.6229
42.77882.47520.68874.39390.82331.5280.01970.17870.4867-0.2659-0.20120.9573-0.4675-0.72120.16490.41320.1993-0.04950.63420.03060.564415.23134.0049154.5222
53.3745-0.0431-2.28353.6944-0.03752.73860.35170.58690.0427-0.934-0.26190.6969-0.2106-0.8499-0.34560.50060.1074-0.27190.8163-0.04580.488215.004120.991135.4566
61.4430.16130.82482.0068-0.20452.35990.1455-0.1947-0.11730.30320.0415-0.14970.15270.1959-0.17420.21850.0124-0.0450.3088-0.03720.284611.9049-1.9482126.4568
71.19320.11740.19811.5751-2.3624.3387-0.0371-0.19630.13280.17080.0345-0.1908-0.46180.3397-0.08320.3095-0.02560.01690.3204-0.0630.30387.79810.0146126.0818
81.01690.28030.43741.7889-0.78892.46860.0516-0.09620.03470.21160.0878-0.2671-0.31350.3649-0.12440.2076-0.0083-0.01150.297-0.06130.268916.76074.5757121.9065
91.46450.3140.05971.6723-0.52322.20880.05110.0995-0.1104-0.00540.0426-0.38770.10770.6057-0.07020.25240.0568-0.04790.4419-0.0660.386319.7246-5.1416117.4463
102.5727-1.60910.22543.64750.76382.09680.01550.13440.2768-0.05990.0184-0.4699-0.37340.7786-0.01080.2831-0.09090.01930.5746-0.0510.398323.79998.4232111.0005
112.1720.6627-0.05362.717-0.20810.01730.0181-0.2779-0.04790.5873-0.0554-0.38830.30690.7077-0.08780.28660.0426-0.17730.597-0.02390.420125.9592-2.1612131.6736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 77 )A33 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 158 )A78 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 171 )A159 - 171
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 187 )A172 - 187
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 207 )A188 - 207
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 65 )B30 - 65
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 77 )B66 - 77
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 102 )B78 - 102
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 158 )B103 - 158
10X-RAY DIFFRACTION10chain 'B' and (resid 159 through 184 )B159 - 184
11X-RAY DIFFRACTION11chain 'B' and (resid 185 through 208 )B185 - 208

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