[English] 日本語
Yorodumi
- PDB-7sdd: Structure of the PTP-like myo-inositol phosphatase from Legionell... -

+
Open data


ID or keywords:

Loading...

-
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 / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more