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- PDB-1e9g: STRUCTURE OF INORGANIC PYROPHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 1e9g
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHeikinheimo, P. / Tuominen, V. / Ahonen, A.-K. / Teplyakov, A. / Cooperman, B.S. / Baykov, A.A. / Lahti, R. / Goldman, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Toward a Quantum-Mechanical Description of Metal-Assisted Phosphoryl Transfer in Pyrophosphatase
Authors: Heikinheimo, P. / Tuominen, V. / Ahonen, A.-K. / Teplyakov, A. / Cooperman, B.S. / Baykov, A.A. / Lahti, R. / Goldman, A.
History
DepositionOct 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
Water18,4291023
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-96.37 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.318, 103.087, 116.518
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: (0.7976, 0.6031, 0.015), (0.6031, -0.7977, 0.0045), (0.0147, 0.0055, -0.9999)
Vector: 35.2522, -102.9809, -90.559)

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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)
Cellular location: CYTOPLASM / 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.: 1023 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN PRESENCE OF DIVALENT METAL CATION CATALYSES THE REACTION: PYROPHOSPHATE + H(2)O = 2 ...IN PRESENCE OF DIVALENT METAL CATION CATALYSES THE REACTION: PYROPHOSPHATE + H(2)O = 2 ORTHOPHOSPHATE. MAGNESIUM CONFERS THE HIGHEST ACTIVITY. THREE OF THE 4 DIVALENT CATIONS BOUND PER SUBUNIT ARE REQUIRED FOR ACTIVITY.
Sequence details1WGJ A SWS P00817 283 - 286 NOT IN ATOMS LIST 1WGJ B SWS P00817 283 - 286 NOT IN ATOMS LIST

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 54.73 %
Description: TWO MERGED DATA SETS: THE FIRST COLLECTED SEP-1996, WAVLENGTH 0.891 A, RESOLUTION RANGE 8-1.5 A AND THE SECOND COLLECTED 1997, WAVELENGTH 0.901 A, RESOLUTION RANGE 2.5-1.15 A
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Heikinheimo, P., (1996) Structure, 4, 1491.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 %MPD1drop
230 mMMES1reservoir
31 mM1reservoirMnCl2
41 mMsodium hydrogen phosphate1reservoir
519 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.891
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.891 Å / Relative weight: 1
ReflectionResolution: 1.15→8 Å / Num. obs: 212495 / % possible obs: 85.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.95
Reflection shellResolution: 1.15→1.17 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 75.5
Reflection shell
*PLUS
% possible obs: 75.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
SHELXLphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WGJ

1wgj


Resolution: 1.15→8 Å / Num. parameters: 51975 / Num. restraintsaints: 60843 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4.7% THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
all0.1361 211693 --
obs--85.5 %-
Rfree---RANDOM
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 42 / Occupancy sum hydrogen: 4448 / Occupancy sum non hydrogen: 5562.12
Refinement stepCycle: LAST / Resolution: 1.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4510 0 28 1023 5561
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0.029
X-RAY DIFFRACTIONs_from_restr_planes0.0304
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.108
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d

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