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- PDB-1wgj: STRUCTURE OF INORGANIC PYROPHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1wgj
TitleSTRUCTURE OF INORGANIC PYROPHOSPHATASE
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE / PYROPHOSPHATE PHOSPHOHYDROLASE / MANGANESE
Function / homology
Function and homology information


Cytosolic tRNA aminoacylation / Mitochondrial tRNA aminoacylation / Pyrophosphate hydrolysis / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / nucleus / 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
: / PHOSPHATE ION / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHeikinheimo, P. / Lehtonen, J. / Goldman, A.
Citation
Journal: Structure / Year: 1996
Title: The structural basis for pyrophosphatase catalysis.
Authors: Heikinheimo, P. / Lehtonen, J. / Baykov, A. / Lahti, R. / Cooperman, B.S. / Goldman, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: New Crystal Forms of E. Coli and S. Cerevisiae Soluble Inorganic Pyrophosphatases
Authors: Heikinheimo, P. / Salminen, T. / Cooperman, B.S. / Lahti, R. / Goldman, A.
History
DepositionOct 24, 1996Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,27014
Polymers64,4512
Non-polymers81912
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-94 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 103.800, 117.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INORGANIC PYROPHOSPHATASE / PPASE


Mass: 32225.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PRODUCT COMPLEX
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PPA1 / Plasmid: PKW9 / Gene (production host): PPA1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P00817, inorganic diphosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mMMES1drop
21 mM1dropMnCl2
31 mMsodium hydrogen phosphate1drop
417 %MPD1drop
519 %MPD1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 5.2 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.103
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. obs: 45565 / % possible obs: 89.2 % / Num. measured all: 236904
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.09 Å / % possible obs: 82.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2008 5 %RANDOM
Rwork0.172 ---
obs0.172 40088 82.4 %-
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-8 Å
Luzzati sigma a0.05 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 28 307 4831
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.45
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.111.5
X-RAY DIFFRACTIONx_mcangle_it3.072
X-RAY DIFFRACTIONx_scbond_it4.172
X-RAY DIFFRACTIONx_scangle_it6.692.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.203 194 5.2 %
Rwork0.192 3510 -
obs--61.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_JPP.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARPO4.PROTOPPO4.PRO
X-RAY DIFFRACTION3PARWAT.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.45

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