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- PDB-1pyp: X-RAY DIFFRACTION STUDY OF INORGANIC PYROPHOSPHATASE FROM BAKER,S... -

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Entry
Database: PDB / ID: 1pyp
TitleX-RAY DIFFRACTION STUDY OF INORGANIC PYROPHOSPHATASE FROM BAKER,S YEAST AT THE 3 ANGSTROMS RESOLUTION (RUSSIAN)
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsACID ANHYDRIDE HYDROLASE
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
Inorganic pyrophosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsHarutyunyan, E.H. / Terzyan, S.S. / Vainshtein, B.K.
Citation
Journal: Dokl.Akad.Nauk Sssr / Year: 1981
Title: X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at the 3 Angstroms Resolution (Russian)
Authors: Arutiunian, E.G. / Terzian, S.S. / Voronova, A.A. / Kuranova, I.P. / Smirnova, E.A. / Vainstein, B.K. / Hohne, W.E. / Hansen, G.
#1: Journal: Dokl.Biochem.(Engl.Transl.) / Year: 1981
Title: X-Ray Structural Investigation of Inorganic Pyrophosphatase from Baker,S Yeast at 3 Angstroms Resolution
Authors: Arutyunyan, E.G. / Terzyan, S.S. / Voronova, A.A. / Kuranova, I.P. / Smirnova, E.A. / Vainshtein, B.K. / Hoehne, W.E. / Hansen, G.
#2: Journal: Kristallografiya / Year: 1980
Title: X-Ray Structural Investigation of Inorganic Pyrophosphatase of Baker Yeast. II. Phase Calculation and Structure Model at 6 Angstroms Resolution (Russian)
Authors: Makhaldiani, V.V. / Smirnova, E.A. / Voronova, A.A. / Tovbis, A.B. / Kuranova, I.P. / Haratyunyan, E.G. / Vainshtein, B.K. / Bienwald, B. / Hansen, G. / Hoehne, W.E.
#3: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1980
Title: X-Ray Structural Investigation of Inorganic Pyrophosphatase of Yeasts. II. Calculation of Phases and Structural Model at 6 Angstroms Resolution
Authors: Makhaldianei, V.V. / Smirnova, E.A. / Voronova, A.A. / Tovbis, A.B. / Kuranova, I.P. / Arutyunyan, E.G. / Vainshtein, B.K. / Bienwald, B. / Hansen, G. / Hoehne, W.E.
#4: Journal: Kristallografiya / Year: 1980
Title: X-Ray Structural Investigation of Inorganic Pyrophosphatase of Baker Yeast. I. Growing of Crystals, Production of Derivatives and Determination of the Heavy Atom Positions in Them (Russian)
Authors: Smirnova, E.A. / Makhaldiani, V.V. / Voronova, A.A. / Kuranova, I.P. / Harutyunyan, E.G. / Vainshtein, B.K. / Heitmann, P. / Hoehne, W.E.
#5: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1980
Title: X-Ray Structural Investigation of Inorganic-Pyrophosphatase of Yeasts. I. Growth of Crystals, Formation of Derivatives, and Determination of the Positions of Their Heavy Atoms
Authors: Smirnova, E.A. / Makhaldiani, V.V. / Voronova, A.A. / Kuranova, I.P. / Arutyunyan, E.G. / Vainshtein, B.K. / Heitmann, P. / Hoehne, W.E.
#6: Journal: Dokl.Akad.Nauk Sssr / Year: 1978
Title: X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at the 6 Angstroms Resolution (Russian)
Authors: Makhaldiani, V.V. / Smirnova, E.A. / Voronova, A.A. / Kuranova, I.P. / Arutiunian, E.G. / Vainstein, B.K. / Hoehne, W.E. / Binwald, B. / Hansen, G.
#7: Journal: Dokl.Biochem.(Engl.Transl.) / Year: 1978
Title: X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at a Resolution of 6 Angstroms
Authors: Makhaldiani, V.V. / Smirnova, E.A. / Voronova, A.A. / Kuranova, I.P. / Arutyunyan, E.G. / Vainshtein, B.K. / Hoehne, W. / Binwald, B. / Hansen, G.
#8: Journal: J.Biol.Chem. / Year: 1978
Title: Covalent Structural Analysis of Yeast Inorganic Pyrophosphatase
Authors: Cohen, S.A. / Sterner, R. / Keim, P.S. / Heinrikson, R.L.
History
DepositionFeb 3, 1983Processing site: BNL
Revision 1.0Oct 27, 1983Provider: 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE SIX-STRANDED BETA-SHEET *BAR* PRESENTED ON SHEET RECORDS BELOW IS ACTUALLY A FIVE- ...SHEET THE SIX-STRANDED BETA-SHEET *BAR* PRESENTED ON SHEET RECORDS BELOW IS ACTUALLY A FIVE-STRANDED BETA-BARREL. THIS IS DENOTED BY HAVING THE FIRST STRAND RECUR AS THE LAST. SHEET III IS A BIFURCATED SHEET. THE THIRD STRAND CONTAINS A BETA-TURN FROM RESIDUES 204-207. TO REPRESENT THIS, TWO SETS OF SHEET RECORDS (S3A, S3B) ARE PRESENTED BELOW, WHICH DIFFER ONLY IN THE THIRD STRAND.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)64,1582
Polymers64,1582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-14 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.230, 70.290, 95.470
Angle α, β, γ (deg.)90.00, 90.00, 99.59
Int Tables number4
Space group name H-MP1121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.965279, -0.156618, -0.209069), (-0.156618, -0.293543, 0.943029), (-0.209064, 0.943029, 0.258821)
Vector: 60.39569, 92.63284, -59.36417)
DetailsTHE TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS BELOW WILL YIELD COORDINATES FOR THE OTHER MOLECULE IN THE ASYMMETRIC UNIT WHEN APPLIED TO THE COORDINATES IN THIS ENTRY.

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Components

#1: Protein INORGANIC PYROPHOSPHATASE


Mass: 32079.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00817, inorganic diphosphatase

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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: 54.3 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 3 Å
Details: FOR PHASE DETERMINATION THREE ISOMORPHOUS HEAVY ATOM DERIVATIVES WERE USED. REFINEMENT OF THE PHASES WAS DONE USING MOLECULAR SYMMETRY.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 0 0 4472

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