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- PDB-4wty: Structure of the PTP-like myo-inositol phosphatase from Selenomon... -

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Basic information

Entry
Database: PDB / ID: 4wty
TitleStructure of the PTP-like myo-inositol phosphatase from Selenomonas ruminantium in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate
ComponentsMYO-INOSITOL PHOSPHOHYDROLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like ...Alpha-Beta Plaits - #1690 / Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / Myo-inositol hexaphosphate phosphohydrolase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBruder, L.M. / Mosimann, S.C.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Foundation for Innovation Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Citation
Journal: To Be Published
Title: Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate
Authors: Bruder, L.M. / Mosimann, S.C.
#1: Journal: J. Biol. Chem. / Year: 2012
Title: Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases.
Authors: Gruninger, R.J. / Dobing, S. / Smith, A.D. / Bruder, L.M. / Selinger, L.B. / Wieden, H.J. / Mosimann, S.C.
#2: Journal: FEBS J. / Year: 2008
Title: Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr.
Authors: Gruninger, R.J. / Selinger, L.B. / Mosimann, S.C.
#3: Journal: Protein Sci. / Year: 2007
Title: Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase.
Authors: Puhl, A.A. / Gruninger, R.J. / Greiner, R. / Janzen, T.W. / Mosimann, S.C. / Selinger, L.B.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYO-INOSITOL PHOSPHOHYDROLASE
B: MYO-INOSITOL PHOSPHOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,84811
Polymers78,2602
Non-polymers1,5889
Water11,944663
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-20 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.830, 138.150, 80.580
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYO-INOSITOL PHOSPHOHYDROLASE


Mass: 39130.000 Da / Num. of mol.: 2 / Fragment: UNP residues 28-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: phyA / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7WUJ1
#2: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16O18P4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 3.18 Å3/Da / Density % sol: 61.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: PEG 8000, sodium chloride, sodium acetate, beta-mercapto ethanol,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→43.06 Å / Num. obs: 56995 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 5.8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimlessdata scaling
MOLREPphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMJ

3mmj


Resolution: 2.1→43.06 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.8 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17538 1797 3.2 %RANDOM
Rwork0.15666 ---
obs0.15724 55187 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.514 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20.38 Å2
2---1 Å2-0 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 93 663 5870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195408
X-RAY DIFFRACTIONr_bond_other_d00.025005
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.9517335
X-RAY DIFFRACTIONr_angle_other_deg0.586311505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1295636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24422.655275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85515885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1481551
X-RAY DIFFRACTIONr_chiral_restr0.0570.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216071
X-RAY DIFFRACTIONr_gen_planes_other00.021344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.682.292535
X-RAY DIFFRACTIONr_mcbond_other2.672.2882534
X-RAY DIFFRACTIONr_mcangle_it3.8963.4163174
X-RAY DIFFRACTIONr_mcangle_other3.8983.4183175
X-RAY DIFFRACTIONr_scbond_it4.3052.8682873
X-RAY DIFFRACTIONr_scbond_other4.2972.8692873
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6524.0794162
X-RAY DIFFRACTIONr_long_range_B_refined9.75523.56129344
X-RAY DIFFRACTIONr_long_range_B_other9.71323.43329003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 148 -
Rwork0.224 4021 -
obs--99.98 %

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