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- PDB-7k6y: Structure of the PTP-like myo-inositol phosphatase from Desulfovi... -

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Basic information

Entry
Database: PDB / ID: 7k6y
TitleStructure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus (high salt)
ComponentsMyo-inositol phosphohydrolase
KeywordsHYDROLASE / phosphatase-like myo-inositol phosphatase / phosphate binding loop / D.magneticus PTPLP (PhyA) / PTPLP / myo-inositol phosphate / myo-inositol phosphohydrolase / myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA / phytase / protein tyrosine phosphatase / PTP
Function / homologyInositol hexakisphosphate / Inositol hexakisphosphate / dephosphorylation / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like / ACETATE ION / Tyrosine specific protein phosphatases domain-containing protein
Function and homology information
Biological speciesDesulfovibrio magneticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVan Herk, P.H. / Cleland, C.P. / Mosimann, S.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus (high salt)
Authors: Cleland, C.P. / Van Herk, P.H. / Mosimann, S.C.
History
DepositionSep 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 24, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Oct 18, 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: Myo-inositol phosphohydrolase
B: Myo-inositol phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,91213
Polymers65,8742
Non-polymers1,03811
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-147 kcal/mol
Surface area22210 Å2
Unit cell
Length a, b, c (Å)61.530, 130.890, 137.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Myo-inositol phosphohydrolase


Mass: 32937.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio magneticus (bacteria) / Gene: DMR_16880 / Production host: Escherichia coli (E. coli) / References: UniProt: C4XPJ9

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Non-polymers , 5 types, 393 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1 / Details: lithium sulfate, sodium acetate, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97959 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.75→37.48 Å / Num. obs: 56203 / % possible obs: 100 % / Redundancy: 5.4 % / Biso Wilson estimate: 23.71 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.3
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 3043 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F41

3f41


Resolution: 1.75→37.48 Å / SU ML: 0.2125 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0956 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2266 1732 3.09 %
Rwork0.1898 54391 -
obs0.1909 56123 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 58 382 4601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534362
X-RAY DIFFRACTIONf_angle_d0.74455941
X-RAY DIFFRACTIONf_chiral_restr0.0442642
X-RAY DIFFRACTIONf_plane_restr0.0043795
X-RAY DIFFRACTIONf_dihedral_angle_d9.65292588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.3421400.29624493X-RAY DIFFRACTION99.81
1.8-1.860.26461140.26684515X-RAY DIFFRACTION99.89
1.86-1.930.28041540.24464450X-RAY DIFFRACTION99.89
1.93-20.26331370.2344502X-RAY DIFFRACTION99.98
2-2.090.27041330.224509X-RAY DIFFRACTION99.94
2.09-2.20.28041780.21984468X-RAY DIFFRACTION99.96
2.2-2.340.24951260.20674528X-RAY DIFFRACTION99.96
2.34-2.520.23581400.19234508X-RAY DIFFRACTION99.98
2.52-2.780.23341670.18244540X-RAY DIFFRACTION100
2.78-3.180.20721540.17034529X-RAY DIFFRACTION100
3.18-4.010.17991290.15264620X-RAY DIFFRACTION100
4.01-37.480.20581600.17924729X-RAY DIFFRACTION99.53

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