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- PDB-1e6a: Fluoride-inhibited substrate complex of Saccharomyces cerevisiae ... -

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Basic information

Entry
Database: PDB / ID: 1e6a
TitleFluoride-inhibited substrate complex of Saccharomyces cerevisiae inorganic pyrophosphatase
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsPHOSPHORYL TRANSFER / HYDROLYSIS
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
FLUORIDE ION / : / PHOSPHATE ION / PYROPHOSPHATE 2- / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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. U.S.A. / 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
DepositionAug 9, 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 2.0Dec 12, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.label_alt_id / _citation.journal_abbrev ..._atom_site.label_alt_id / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 2.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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)65,49317
Polymers64,4512
Non-polymers1,04215
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.770, 102.340, 115.630
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: (0.8028, 0.5963, 0.0028), (0.5963, -0.8028, 0.0009), (0.0028, 0.0009, -1)
Vector: 33.8508, -101.9184, -89.2511)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein INORGANIC PYROPHOSPHATASE / / 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)
Cellular location: CYTOPLASM / Gene: PPA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL2-BLUEB / References: UniProt: P00817, inorganic diphosphatase

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Non-polymers , 6 types, 663 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsREACTION CARRIED OUT IN PRESENCE OF DIVALENT METAL CATION PYROPHOSPHATE + H(2)O = 2 ORTHOPHOSPHATE

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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: 2.65 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 19 MICROLITER SITTING DROPS 16-20% MPD, 30 MM MES, PH 6.0, 1 MM MNCL2, 0.5 MM NA2P2O7H2, 5 MM NAF,10 MG/ML PROTEIN
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mMMes1drop
21 mM1dropMnCl2
35 mM1dropNaF
41 mMNaPPi1drop
516 %MPD1drop
618-20 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.0039
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0039 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 53366 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 1.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.247 / % possible all: 92.6
Reflection shell
*PLUS
% possible obs: 92.6 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
HKLdata reduction
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 231011.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: REFINEMENT STARTED USING X-PLOR VERSION 3.851, CONTINUED BY CNS 0.4 AND FINISHED BY CNS 05
RfactorNum. reflection% reflectionSelection details
Rfree0.182 3711 4.2 %RANDOM
Rwork0.155 ---
obs0.155 87817 85.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.344 Å2 / ksol: 0.514096 e/Å3
Displacement parametersBiso mean: 10.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2--0.09 Å20 Å2
3----1.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4475 0 39 648 5162
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.671.5
X-RAY DIFFRACTIONc_mcangle_it1.022
X-RAY DIFFRACTIONc_scbond_it2.862
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.201 473 3.9 %
Rwork0.179 11514 -
obs--69.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMTOPH19.ION
X-RAY DIFFRACTION3ION.PARAMPOP_XPLOR
X-RAY DIFFRACTION4POP_XPLORTOPPO4.PR
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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