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- PDB-1m38: Structure of Inorganic Pyrophosphatase -

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Basic information

Entry
Database: PDB / ID: 1m38
TitleStructure of Inorganic Pyrophosphatase
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE / PYROPHOSPHATE PHOSPHOHYDROLASE / COBALT
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKuranova, I.P. / Polyakov, K.M. / Levdikov, V.M. / Smirnova, E.A. / Hohne, W.E. / Lamzin, V.S. / Meijers, R.
Citation
Journal: CRYSTALLOGRAPHY REPORTS / Year: 2003
Title: Three-dimensional structure of Saccharomyces cerevisiae inorganic pyrophosphatase complexed with cobalt and phosphate ions
Authors: Kuranova, I.P. / Polyakov, K.M. / Smirnova, E.A. / Hohne, W.E. / Lamzin, V.S. / Meijers, R.
History
DepositionJun 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,22510
Polymers64,6812
Non-polymers5448
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-102 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.690, 93.230, 69.840
Angle α, β, γ (deg.)90.00, 99.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein INORGANIC PYROPHOSPHATASE / / Ipp1p / Pyrophosphate phospho-hydrolase / PPase


Mass: 32340.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00817, inorganic diphosphatase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.26 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: mes-buffer, cobalt chloride, imidodiphosphate, 2-methyl-2,4-pentadiole, pH 6.5, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.77→17.6 Å / Num. obs: 63474 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.65 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.037

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
BLANCmodel building
REFMACrefinement
CCP4(TRUNCATE)data scaling
BLANCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→17.59 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1211 2 %RANDOM
Rwork0.1932 ---
all0.1932 63474 --
obs0.1932 63474 100 %-
Displacement parametersBiso mean: 29.67 Å2
Refine analyzeLuzzati coordinate error obs: 0.117 Å
Refinement stepCycle: LAST / Resolution: 1.8→17.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 0 17 666 5234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_angle_refined_deg2.561
X-RAY DIFFRACTIONr_chiral_restr0.171
LS refinement shellResolution: 1.8→1.846 Å
RfactorNum. reflection
Rfree0.296 91
Rwork0.209 -
obs-4366

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