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- PDB-8prk: THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISI... -

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Basic information

Entry
Database: PDB / ID: 8prk
TitleTHE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS
ComponentsPROTEIN (INORGANIC PYROPHOSPHATASE)
KeywordsHYDROLASE / ENZYME MECHANISM / IORGANIC PYROPHOSPHATASE / MUTANT STRUCTURES / 2-METAL ION MECHANISM
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: 1.85 Å
AuthorsTuominen, V. / Heikinheimo, P. / Kajander, T. / Torkkel, T. / Hyytia, T. / Kapyla, J. / Lahti, R. / Cooperman, B.S. / Goldman, A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The R78K and D117E active-site variants of Saccharomyces cerevisiae soluble inorganic pyrophosphatase: structural studies and mechanistic implications.
Authors: Tuominen, V. / Heikinheimo, P. / Kajander, T. / Torkkel, T. / Hyytia, T. / Kapyla, J. / Lahti, R. / Cooperman, B.S. / Goldman, A.
#1: 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.
#2: Journal: Eur.J.Biochem. / Year: 1996
Title: A Site-Directed Mutagenesis Study of Saccharomyces Cerevisiae Pyrophosphatase Functional Conservation of the Active Site of Soluble Inorganic Pyrophosphatases
Authors: Heikinheimo, P. / Pohjanjoki, P. / Helminen, A. / Tasanen, M. / Cooperman, B.S. / Goldman, A. / Baykov, A. / Lahti, R.
History
DepositionSep 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (INORGANIC PYROPHOSPHATASE)
B: PROTEIN (INORGANIC PYROPHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,17710
Polymers64,6572
Non-polymers5208
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.700, 102.300, 117.000
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: (0.799085, 0.601106, 0.011616), (0.601138, -0.799145, 0.000919), (0.009835, 0.006248, -0.999932)
Vector: 34.7983, -102.6667, -90.4628)

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Components

#1: Protein PROTEIN (INORGANIC PYROPHOSPHATASE) / PPASE


Mass: 32328.555 Da / Num. of mol.: 2 / Mutation: R78K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cellular location: CYTOPLASM / Gene: PPA1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / Keywords: PRODUCT COMPLEX / References: UniProt: P00817, inorganic diphosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.71 Å3/Da / Density % sol: 54.7 %
Crystal growpH: 6
Details: 17-19 % MPD 25 MM MES, PH 6.0 1 MM MNCL2 0.5 MM NA2HPO4 10 MG/ML PROTEIN
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225 mMMES1drop
31 mM1dropMnCl2
40.5 mMsodium hydrogen phosphate1drop
517 %(v/v)MPD1drop
619 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.891
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.891 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 54387 / % possible obs: 89.3 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.8
Reflection shellResolution: 1.85→1.88 Å / % possible all: 92.5
Reflection
*PLUS
Rmerge(I) obs: 0.062 / Num. measured all: 524728
Reflection shell
*PLUS
% possible obs: 92.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WGJ

1wgj


Resolution: 1.85→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4376 8.6 %RANDOM
Rwork0.19 ---
obs0.19 51133 85.2 %-
Displacement parametersBiso mean: 12 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4437 0 2367 2367 9171
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.5
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_d1.37
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.231.5
X-RAY DIFFRACTIONx_mcangle_it1.72
X-RAY DIFFRACTIONx_scbond_it2.192
X-RAY DIFFRACTIONx_scangle_it3.052.5
LS refinement shellResolution: 1.85→1.88 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 182 7.7 %
Rwork0.237 2177 -
obs--80.1 %
Xplor file
Refine-IDSerial noTopol fileParam file
X-RAY DIFFRACTION1TOPHCSDX.PRO
X-RAY DIFFRACTION2TOPPO4.PRPROTEIN_REP.PARAM
X-RAY DIFFRACTION3TOPH11.WATPARAMETER.ELEMENTS
X-RAY DIFFRACTION4TOPOLOGY.ELEMENTSPARAM11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / 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_deg1.37

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