[English] 日本語
Yorodumi
- PDB-9n58: Structure of the PTP-like myo-inositol phosphatase from Solidesul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n58
TitleStructure of the PTP-like myo-inositol phosphatase from Solidesulfovibrio magneticus in complex with myo-inositol hexakisphosphate
ComponentsTyrosine specific protein phosphatases domain-containing protein
KeywordsHYDROLASE / phosphatase-like myo-inositol phosphatase / phosphate binding loop / S.magneticus PTPLP (PhyA) / PTPLP / myo-inositol phosphate / myo-inositol phosphohydrolase / myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA / phytase / protein tyrosine phosphatase / PTP / IP6 / InsP6 / myo-inositol hexakisphosphate / phytate
Function / homologyInositol hexakisphosphate / Inositol hexakisphosphate / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like / INOSITOL HEXAKISPHOSPHATE / Tyrosine specific protein phosphatases domain-containing protein
Function and homology information
Biological speciesSolidesulfovibrio magneticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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: Novel Structure of PhyA from Solidesulfovibrio magneticus indicates the phosphate-binding loop influences InsP6 binding modes and substrate specificity
Authors: Cleland, C.P. / Mosimann, S.C.
History
DepositionFeb 3, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 12, 2025ID: 7K6W
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine specific protein phosphatases domain-containing protein
B: Tyrosine specific protein phosphatases domain-containing protein
C: Tyrosine specific protein phosphatases domain-containing protein
D: Tyrosine specific protein phosphatases domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,9808
Polymers131,3404
Non-polymers2,6404
Water20,7171150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-76 kcal/mol
Surface area40280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.019, 97.339, 104.055
Angle α, β, γ (deg.)90.000, 92.583, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Tyrosine specific protein phosphatases domain-containing protein


Mass: 32835.008 Da / Num. of mol.: 4 / Mutation: C241S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solidesulfovibrio magneticus (bacteria)
Gene: DMR_16880 / Production host: Escherichia coli (E. coli) / References: UniProt: C4XPJ9
#2: Chemical
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: PEG 4000 and 1000, 2-methyl-2,4-pentanediol, carboxylates, sodium acetate

-
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 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→24.55 Å / Num. obs: 86432 / % possible obs: 98.8 % / Redundancy: 3 % / Biso Wilson estimate: 19.07 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.84
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.322 / Num. unique obs: 8645 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisPro41.110adata reduction
CrysalisPro41.110adata scaling
MOLREP1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→24.55 Å / SU ML: 0.2055 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 1999 2.31 %
Rwork0.1799 84386 -
obs0.1806 86385 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.78 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8217 0 144 1150 9511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028595
X-RAY DIFFRACTIONf_angle_d0.549911725
X-RAY DIFFRACTIONf_chiral_restr0.03661279
X-RAY DIFFRACTIONf_plane_restr0.0041541
X-RAY DIFFRACTIONf_dihedral_angle_d11.50493165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.26931340.22815961X-RAY DIFFRACTION97.8
2.1-2.160.24941380.22335948X-RAY DIFFRACTION98.24
2.16-2.220.23921670.21025967X-RAY DIFFRACTION98.47
2.22-2.290.2891240.20416013X-RAY DIFFRACTION98.97
2.29-2.380.24251520.20616057X-RAY DIFFRACTION99.33
2.38-2.470.22781350.19566028X-RAY DIFFRACTION99.39
2.47-2.580.23641550.19526079X-RAY DIFFRACTION99.7
2.58-2.720.22611440.18996068X-RAY DIFFRACTION99.9
2.72-2.890.22561450.18926083X-RAY DIFFRACTION99.94
2.89-3.110.19411430.18226066X-RAY DIFFRACTION99.73
3.11-3.420.22041480.17466089X-RAY DIFFRACTION99.55
3.42-3.920.19621290.15486078X-RAY DIFFRACTION99.07
3.92-4.930.15191450.14046013X-RAY DIFFRACTION97.84
4.93-24.550.16191400.17145936X-RAY DIFFRACTION95.38

+
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