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- PDB-4lug: Crystal structure of Inorganic Pyrophosphatase PPA1 from Arabidop... -

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Basic information

Entry
Database: PDB / ID: 4lug
TitleCrystal structure of Inorganic Pyrophosphatase PPA1 from Arabidopsis thaliana
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / Hydrolysis of pyrophosphate / Magnesium ion binding / Metal binding
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 / cytoplasm / cytosol
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
Soluble inorganic pyrophosphatase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsGrzechowiak, M. / Ruszkowski, M. / Sikorski, M. / Jaskolski, M.
Citation
Journal: To be Published
Title: Crystal structure of Inorganic pyrophosphatase PPA1 from Arabidopsis thaliana
Authors: Grzechowiak, M. / Ruszkowski, M. / Sikorski, M. / Jaskolski, M.
#1: Journal: Febs Lett. / Year: 2004
Title: Identification of an Arabidopsis inorganic pyrophosphatase capable of being imported into chloroplasts
Authors: Schulze, S. / Mant, A. / Kossmann, J. / Lloyd, J.R.
#2: Journal: Plant Sci. / Year: 2007
Title: Characterization of two soluble inorganic pyrophosphatases from Arabidopsis thaliana
Authors: Navarro-De la Sancha, E. / Coello-Coutino, M.P. / Valencia-Turcotte, L.G. / Hernandez-Dominguez, E.E. / Trejo-Yepes, G. / Rodriguez-Sotres, R.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6284
Polymers41,5822
Non-polymers462
Water3,117173
1
A: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4426
Polymers62,3733
Non-polymers693
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 area4840 Å2
ΔGint-69 kcal/mol
Surface area22300 Å2
MethodPISA
2
B: Inorganic pyrophosphatase
hetero molecules

B: Inorganic pyrophosphatase
hetero molecules

B: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4426
Polymers62,3733
Non-polymers693
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 area4810 Å2
ΔGint-69 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.02, 82.02, 175.08
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-493-

HOH

21B-499-

HOH

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Components

#1: Protein Inorganic pyrophosphatase / At1g01050/T25K16_5


Mass: 20790.850 Da / Num. of mol.: 2 / Fragment: UNP residues 33-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PPa1 / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Magic / References: UniProt: Q93V56, inorganic diphosphatase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M succinic acid, 15%(w/v) PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 17, 2012 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.93→41.01 Å / Num. all: 33078 / Num. obs: 32974 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 40.84 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.93-2.050.8410.5982.0417337535352740.7198.5
2.05-2.190.4330.3324.1919303500550000.38799.9
2.19-2.360.2340.187.4818128469046870.20999.9
2.36-2.590.1480.12210.8616765431543140.142100
2.59-2.890.0790.06718.2415128387938790.078100
2.89-3.340.0370.03930.2913378341834170.045100
3.34-4.080.0210.02645.611266291429120.0399.9
4.08-5.740.0150.02155.398649224022370.02499.9
5.74-410.0120.01759.024842126412540.0299.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.72 Å41.01 Å
Translation3.72 Å41.01 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TWL

1twl


Resolution: 1.93→41.01 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.2 / Phase error: 22.21 / Stereochemistry target values: Engh & Huber / Details: hydrogen atoms were added at riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 1005 3.05 %RANDOM
Rwork0.1555 ---
all0.1568 33078 --
obs0.1568 32971 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.77 Å2 / Biso mean: 44.49 Å2 / Biso min: 18.38 Å2
Refinement stepCycle: LAST / Resolution: 1.93→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 2 173 3015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192925
X-RAY DIFFRACTIONf_angle_d1.3963995
X-RAY DIFFRACTIONf_chiral_restr0.088433
X-RAY DIFFRACTIONf_plane_restr0.008514
X-RAY DIFFRACTIONf_dihedral_angle_d15.3711109
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-2.030.2681430.2214542468598
2.03-2.160.2461430.18745684711100
2.16-2.330.211440.16345664710100
2.36-2.560.2261440.16245694713100
2.56-2.930.2231440.16645934737100
2.93-3.690.1981440.15545554699100
3.69-41.020.1681430.13745734716100
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)
11.77880.730.83713.06051.49413.9580.07540.3002-0.1424-0.5832-0.00070.41010.0343-0.2818-0.03990.25690.0124-0.12110.28610.0130.336928.265321.88884.4579
22.33020.27570.15763.61182.12197.890.03260.59160.1291-0.8099-0.2210.3257-0.8481-0.76060.01770.45510.0524-0.04120.37640.07950.333633.149333.669984.0042
31.23140.29510.5252.35281.01243.12640.06110.18460.0436-0.6944-0.15690.6388-0.694-0.55840.02710.40.1063-0.11190.37750.03410.436124.07628.100588.2725
43.1233-0.0721-0.28892.02051.17163.50740.10090.16890.1544-0.2678-0.11990.4573-0.2081-0.71950.00740.2992-0.0213-0.11180.42090.04270.423621.985221.923390.7669
53.1175-1.4841-1.27390.85961.03561.72380.0229-0.3317-0.83770.2082-0.04851.11970.4161-0.47260.09470.348-0.1964-0.01830.56970.00550.705619.841410.170597.276
63.91810.23590.27843.50521.01083.54630.1854-0.05330.6106-0.1019-0.02181.0081-0.6405-1.10330.10590.37960.1328-0.04180.55860.060.522317.09931.772799.1535
71.8114-0.43120.29382.14281.59161.74660.03110.5486-0.0518-0.8106-0.38320.7748-0.484-0.7364-0.23740.46880.1197-0.34970.8376-0.02670.774814.840621.031478.9806
81.8362-0.63390.9582.5034-1.33023.58010.1133-0.1231-0.07120.32950.0611-0.223-0.08020.2883-0.14010.1803-0.0172-0.05110.2539-0.06120.257411.44021.528166.9224
90.9376-0.65831.41542.7037-1.70434.7751-0.0059-0.02740.10870.32290.0094-0.4426-0.44060.4683-0.01570.2002-0.0412-0.00790.3143-0.06330.314616.81464.687663.0461
104.23960.4-0.462.626-0.57953.53950.01540.3789-0.1692-0.00360.0766-0.61590.09110.8019-0.06050.22080.0721-0.06720.4353-0.07250.378719.8091-5.06658.4906
118.0297-3.52790.493.1296-0.89463.45080.12930.22090.7689-0.09340.0001-0.9282-0.57551.2242-0.1120.3083-0.11960.04110.6688-0.06150.463123.75898.468452.0335
122.71170.7017-0.6322.44-0.9611.02140.0274-0.1102-0.02260.5488-0.1129-0.6310.00370.76490.15370.32540.0473-0.2590.5908-0.05390.570626.1895-2.088172.8298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 33:65 )A33 - 65
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 66:77 )A66 - 77
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 78:102 )A78 - 102
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 103:142 )A103 - 142
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 143:158 )A143 - 158
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 159:184 )A159 - 184
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 185:207 )A185 - 207
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 33:77 )B33 - 77
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 78:102 )B78 - 102
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 103:158 )B103 - 158
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 159:184 )B159 - 184
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 185:208 )B185 - 208

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