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- PDB-2ik1: Yeast inorganic pyrophosphatase variant Y93F with magnesium and p... -

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Basic information

Entry
Database: PDB / ID: 2ik1
TitleYeast inorganic pyrophosphatase variant Y93F with magnesium and phosphate
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / INORGANIC PYROPHOSPHATASE / STRUCTURE-FUNCTION / MUTAGENESIS
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOksanen, E. / Ahonen, A.K. / Tuominen, H. / Tuominen, V. / Lahti, R. / Goldman, A. / Heikinheimo, P.
CitationJournal: Biochemistry / Year: 2007
Title: A Complete Structural Description of the Catalytic Cycle of Yeast Pyrophosphatase.
Authors: Oksanen, E. / Ahonen, A.K. / Tuominen, H. / Tuominen, V. / Lahti, R. / Goldman, A. / Heikinheimo, P.
History
DepositionOct 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_ref_seq_dif.details
Revision 1.4Aug 30, 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

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6876
Polymers64,4192
Non-polymers2684
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-41 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.770, 93.541, 69.439
Angle α, β, γ (deg.)90.00, 99.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase


Mass: 32209.375 Da / Num. of mol.: 2 / Mutation: Y93F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IPP1 / Plasmid: PKW9 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P00817, inorganic diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 16% MPD, 10 MM MGCL2, 1 MM PO4-, PH 6.0, VAPOR DIFFUSION, TEMPERATURE 277K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 21, 2001 / Details: MULTILAYER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 67570 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 7.9
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.346 / % possible all: 94.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HUK

1huk


Resolution: 1.7→19.69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.78 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19007 3417 5.1 %RANDOM
Rwork0.16663 ---
obs0.16782 64116 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.081 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4406 0 15 505 4926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224528
X-RAY DIFFRACTIONr_bond_other_d0.0020.024006
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9496158
X-RAY DIFFRACTIONr_angle_other_deg0.81539418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024990
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02846
X-RAY DIFFRACTIONr_nbd_refined0.2220.2846
X-RAY DIFFRACTIONr_nbd_other0.2450.24634
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.22467
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2357
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0570.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.330.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7821.52781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40324517
X-RAY DIFFRACTIONr_scbond_it2.30631747
X-RAY DIFFRACTIONr_scangle_it3.7494.51641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 215
Rwork0.31 4572

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