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- PDB-1ypp: ACID ANHYDRIDE HYDROLASE -

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Basic information

Entry
Database: PDB / ID: 1ypp
TitleACID ANHYDRIDE HYDROLASE
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE
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 / Resolution: 2.4 Å
AuthorsHarutyunyan, E.H. / Kuranova, I.P. / Lamzin, V.S. / Dauter, Z. / Wilson, K.S.
Citation
Journal: Eur.J.Biochem. / Year: 1996
Title: X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate.
Authors: Harutyunyan, E.H. / Kuranova, I.P. / Vainshtein, B.K. / Hohne, W.E. / Lamzin, V.S. / Dauter, Z. / Teplyakov, A.V. / Wilson, K.S.
#1: Journal: Crystallography reports / Year: 1996
Title: Structure of Inorganic Pyrophosphatase from E. Coli and its Complex with a Mn2+ Ion at 2.2 Angstroms Resolution
Authors: Harutyunyan, E.H. / Oganessyan, V.Yu. / Oganessyan, N.N. / Terzyan, S.S. / Popov, A.N. / Rubinskiy, S.V. / Vainshtein, B.K. / Nazarova, T.I. / Kurilova, S.A. / Vorobyova, N.N. / Avaeva, S.M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: New Crystal Forms of Escherichia Coli and Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatases
Authors: Heikineimo, P. / Salminen, T. / Lahti, R. / Cooperman, B. / Goldman, A.
#3: Journal: Protein Sci. / Year: 1994
Title: Crystal Structure of Inorganic Pyrophosphatase from Thermus Thermophilus
Authors: Teplyakov, A. / Obmolova, G. / Wilson, K.S. / Ishii, K. / Kaji, H. / Samejima, T. / Kuranova, I.
#4: Journal: Protein Eng. / Year: 1994
Title: The Structure of E.Coli Soluble Inorganic Pyrophosphatase at 2.7 A Resolution
Authors: Kankare, J. / Neal, G.S. / Salminen, T. / Glumhoff, T. / Cooperman, B.S. / Lahti, R. / Goldman, A.
#5: Journal: Eur.J.Biochem. / Year: 1992
Title: Two Pathways of Pyrophosphate Hydrolysis and Synthesis by Yeast Inorganic Pyrophosphatase
Authors: Baykov, A.A. / Shestakov, A.S.
#6: Journal: Kristallografiya / Year: 1991
Title: Crystal Structure of Mnpi Complex of Yeast Inorganic Pyrophosphatase at 2.35 Angstroms Resolution (Russian)
Authors: Chirgadze, N.Yu. / Kuranova, I.P. / Nevskaya, N.A. / Teplyakov, A.V. / Wilson, K.S. / Strokopytov, B.N. / Harutyunyan, E.H. / Hohne, W.E.
#7: Journal: Kristallografiya / Year: 1990
Title: The Growing of Crystals of Inorganic Pyrophosphatase from Yeast with Metal Ions and Phosphate (Russian)
Authors: Kuranova, I.P. / Smirnova, E.A. / Chirgadze, N.Yu.
#8: Journal: Bioorg.Khim. / Year: 1986
Title: A Conformational Hypothesis of the Trans-Ligation of Metals which Activate Pyrophosphatase and Related Enzymes (Russian)
Authors: Kuranova, I.P. / Sokolov, V.I.
#9: Journal: Bioorg.Khim. / Year: 1984
Title: Inorganic Pyrophosphatase from Yeast at 3 A Resolution (Russian)
Authors: Terzyan, S.S. / Voronova, A.A. / Smirnova, E.A. / Kuranova, I.P. / Nekrasov, Yu.V. / Harutyunyan, E.G. / Vainshtein, B.K. / Hohne, W. / Hansen, G.
#10: Journal: J.Biol.Chem. / Year: 1984
Title: Investigations of the Metal Ion-Binding Sites of Yeast Inorganic Pyrophosphatase
Authors: Knight, W.B. / Dunaway-Mariano, D. / Ransom, S.C. / Villafranca, J.J.
#11: Journal: Methods Enzymol. / Year: 1982
Title: The Mechanism of Action of Yeast Inorganic Pyrophosphatase
Authors: Cooperman, B.S.
#12: Journal: Eur.J.Biochem. / Year: 1974
Title: Yeast Inorganic Pyrophosphatase: Studies on Metal Binding
Authors: Baykov, A.A. / Avaeva, S.M.
History
DepositionMay 29, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 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_ref_seq_dif / 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_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_ref_seq_dif.details / _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)65,12214
Polymers64,3022
Non-polymers81912
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-97 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.000, 106.200, 56.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99734, -0.0405, -0.06061), (-0.00066, -0.82638, 0.56312), (-0.07289, 0.56166, 0.82415)
Vector: 32.247, 13.439, -3)
DetailsTHE ASYMMETRIC UNIT CONTAINS A DIMER. THE TWO CHEMICALLY IDENTICAL SUBUNITS ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AXIS. ONLY 282 RESIDUES IN BOTH SUBUNITS ARE VISIBLE IN THE ELECTRON DENSITY.

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Components

#1: Protein INORGANIC PYROPHOSPHATASE


Mass: 32151.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: S2 / 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.: 222 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal grow
*PLUS
pH: 6.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.03 MMES11
30.5 mMphosphate11
4MPD11
211Mn2+

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.38
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.095
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 21721 / % possible obs: 79 %
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.44 Å / % possible obs: 62 % / Rmerge(I) obs: 0.199

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→10 Å / σ(F): 0 /
Num. reflection% reflection
obs21721 79 %
Displacement parametersBiso mean: 29.5 Å2
Refine analyzeLuzzati sigma a obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 28 222 4746
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0310.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.62
X-RAY DIFFRACTIONp_mcangle_it43
X-RAY DIFFRACTIONp_scbond_it6.384
X-RAY DIFFRACTIONp_scangle_it9.025
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.2220.15
X-RAY DIFFRACTIONp_singtor_nbd0.2090.3
X-RAY DIFFRACTIONp_multtor_nbd0.2760.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2360.3
X-RAY DIFFRACTIONp_planar_tor3.673
X-RAY DIFFRACTIONp_staggered_tor21.2715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.2820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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