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

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Basic information

Entry
Database: PDB / ID: 7sdb
TitleStructure of the PTP-like myo-inositol phosphatase from Legionella pneumophila str. Paris in complex with myo-inositol hexakisphosphate
ComponentsMyo-inositol phosphohydrolase
KeywordsHYDROLASE / Phytase / PTP fold / myo-inositol phosphate / effector protein
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasm
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 HEXAKISPHOSPHATE / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesLegionella pneumophila str. Paris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 hexakisphosphate
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myo-inositol phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6872
Polymers36,0271
Non-polymers6601
Water7,098394
1
A: Myo-inositol phosphohydrolase
hetero molecules

A: Myo-inositol phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3744
Polymers72,0542
Non-polymers1,3202
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)62.309, 62.456, 95.497
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-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.96 %
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 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→24.08 Å / Num. obs: 25244 / % possible obs: 97.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.14 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.81
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.198 / Num. unique obs: 2528

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisProv41.108adata reduction
CrysalisProv41.108adata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVV

4tvv


Resolution: 2→24.08 Å / SU ML: 0.1607 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.196 1999 7.93 %
Rwork0.164 23200 -
obs0.1666 25199 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.02 Å2
Refinement stepCycle: LAST / Resolution: 2→24.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 36 394 2766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632475
X-RAY DIFFRACTIONf_angle_d0.7373372
X-RAY DIFFRACTIONf_chiral_restr0.0463365
X-RAY DIFFRACTIONf_plane_restr0.0073424
X-RAY DIFFRACTIONf_dihedral_angle_d7.968352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.22011360.17871573X-RAY DIFFRACTION94.73
2.05-2.110.19571390.17241631X-RAY DIFFRACTION97.2
2.11-2.170.20521400.16771622X-RAY DIFFRACTION97.03
2.17-2.240.19811380.1731630X-RAY DIFFRACTION96.72
2.24-2.320.2331440.16741612X-RAY DIFFRACTION96.7
2.32-2.410.18451370.16551633X-RAY DIFFRACTION97.41
2.41-2.520.2351400.16561645X-RAY DIFFRACTION97.92
2.52-2.650.21791440.16261666X-RAY DIFFRACTION98.85
2.65-2.820.21761410.17171672X-RAY DIFFRACTION98.8
2.82-3.040.21251420.1771681X-RAY DIFFRACTION99.24
3.04-3.340.18891480.16281697X-RAY DIFFRACTION99.62
3.34-3.820.16311500.15051712X-RAY DIFFRACTION99.52
3.82-4.810.16131520.14391705X-RAY DIFFRACTION97.84
4.81-24.080.20751480.17491721X-RAY DIFFRACTION94.68

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