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- PDB-2ihp: Yeast inorganic pyrophosphatase with magnesium and phosphate -

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Basic information

Entry
Database: PDB / ID: 2ihp
TitleYeast inorganic pyrophosphatase 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
PHOSPHATE ION / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionSep 27, 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 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,95710
Polymers64,4512
Non-polymers5078
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-70 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.915, 93.549, 69.168
Angle α, β, γ (deg.)90.00, 99.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32225.375 Da / Num. of mol.: 2
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.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 670 / 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: 52.09 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8727 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8727 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. all: 103964 / Num. obs: 103964 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 21.7
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6946 / Rsym value: 0.321 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HUK

1huk


Resolution: 1.5→19.92 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.961 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 5172 5 %RANDOM
Rwork0.162 ---
all0.163 103685 --
obs0.163 103685 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4447 0 27 670 5144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224581
X-RAY DIFFRACTIONr_bond_other_d0.0010.024056
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9626231
X-RAY DIFFRACTIONr_angle_other_deg0.79239536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66925.625208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60215781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8111512
X-RAY DIFFRACTIONr_chiral_restr0.1520.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02848
X-RAY DIFFRACTIONr_nbd_refined0.2250.2875
X-RAY DIFFRACTIONr_nbd_other0.180.24137
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22334
X-RAY DIFFRACTIONr_nbtor_other0.0830.22387
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2480
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.241
X-RAY DIFFRACTIONr_mcbond_it0.9351.52979
X-RAY DIFFRACTIONr_mcbond_other0.1911.51115
X-RAY DIFFRACTIONr_mcangle_it1.29524554
X-RAY DIFFRACTIONr_scbond_it2.12132003
X-RAY DIFFRACTIONr_scangle_it2.944.51677
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 367 -
Rwork0.175 7260 -
obs-7627 100 %

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