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- PDB-7sdd: Structure of the PTP-like myo-inositol phosphatase from Legionell... -

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Basic information

Entry
Database: PDB / ID: 7sdd
TitleStructure of the PTP-like myo-inositol phosphatase from Legionella pneumophila str. Paris in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate
ComponentsMyo-inositol phosphohydrolase
KeywordsHYDROLASE / Phytase / PTP fold / myo-inositol phosphate / IPase
Function / homology
Function and homology information


protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase
Similarity search - Function
Inositol hexakisphosphate / Inositol hexakisphosphate / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / Tyrosine phosphatase II superfamily protein
Similarity search - Component
Biological speciesLegionella pneumophila str. Paris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCleland, 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 Legionella pneumophila str. Paris in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate
Authors: Cleland, C.P. / Mosimann, S.C.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myo-inositol phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5272
Polymers36,0271
Non-polymers5001
Water8,161453
1
A: Myo-inositol phosphohydrolase
hetero molecules

A: Myo-inositol phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0544
Polymers72,0542
Non-polymers1,0002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)62.581, 63.211, 95.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Myo-inositol phosphohydrolase


Mass: 36026.867 Da / Num. of mol.: 1 / Mutation: C231S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila str. Paris (bacteria)
Gene: hopD2, NCTC12000_03020 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A378K9X8, protein-tyrosine-phosphatase
#2: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O18P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100 mM Tris HCl (7.4), 12% PEG 4000, 40 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→25.84 Å / Num. obs: 32744 / % possible obs: 99.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 17.23
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3278

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisProv40.108adata reduction
CrysalisProv40.108adata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVV

4tvv


Resolution: 1.85→25.84 Å / SU ML: 0.1798 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.2618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2049 2003 6.15 %
Rwork0.1814 30576 -
obs0.1829 32579 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.62 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 28 453 2817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462451
X-RAY DIFFRACTIONf_angle_d0.74593333
X-RAY DIFFRACTIONf_chiral_restr0.0466362
X-RAY DIFFRACTIONf_plane_restr0.0066420
X-RAY DIFFRACTIONf_dihedral_angle_d14.0288916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.41441380.34572065X-RAY DIFFRACTION95.12
1.9-1.950.28391400.23942106X-RAY DIFFRACTION97.57
1.95-20.25191370.20872145X-RAY DIFFRACTION98.4
2-2.070.21381390.18412185X-RAY DIFFRACTION99.36
2.07-2.140.18911450.17532137X-RAY DIFFRACTION99.52
2.14-2.230.25781390.19582184X-RAY DIFFRACTION99.15
2.23-2.330.23691450.22632161X-RAY DIFFRACTION98.34
2.33-2.450.22481420.16892156X-RAY DIFFRACTION99.83
2.45-2.610.2081440.16062213X-RAY DIFFRACTION99.83
2.61-2.810.19411410.17432193X-RAY DIFFRACTION99.79
2.81-3.090.20171450.17532214X-RAY DIFFRACTION99.58
3.09-3.540.16781460.16672230X-RAY DIFFRACTION99.75
3.54-4.450.17231470.14932236X-RAY DIFFRACTION99.46
4.45-25.840.17231550.1722351X-RAY DIFFRACTION99.4

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