[English] 日本語
Yorodumi
- PDB-5qdj: PanDDA analysis group deposition -- Crystal structure of PTP1B in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5qdj
TitlePanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000211a
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PanDDA / SGC - Diamond I04-1 fragment screening / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multiconformer
Function / homology
Function and homology information


PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / cytoplasmic side of endoplasmic reticulum membrane ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / positive regulation of protein tyrosine kinase activity / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / MECP2 regulates neuronal receptors and channels / negative regulation of MAP kinase activity / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / protein dephosphorylation / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein phosphatase 2A binding / endosome lumen / insulin receptor binding / Negative regulation of MET activity / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
N-(4-methyl-1,3-thiazol-2-yl)propanamide / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.761 Å
AuthorsKeedy, D.A. / Hill, Z.B. / Biel, J.T. / Kang, E. / Rettenmaier, T.J. / Brandao-Neto, J. / von Delft, F. / Wells, J.A. / Fraser, J.S.
CitationJournal: Elife / Year: 2018
Title: An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.
Authors: Keedy, D.A. / Hill, Z.B. / Biel, J.T. / Kang, E. / Rettenmaier, T.J. / Brandao-Neto, J. / Pearce, N.M. / von Delft, F. / Wells, J.A. / Fraser, J.S.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9785
Polymers37,3461
Non-polymers6334
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint2 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.787, 89.787, 106.539
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 1 / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 37345.562 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: C32S, C92V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-JFP / N-(4-methyl-1,3-thiazol-2-yl)propanamide


Mass: 170.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H10N2OS
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.76→62.808 Å / Num. obs: 95050 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.106 / Χ2: 1.145 / Net I/σ(I): 11.72 / Num. measured all: 491179
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.76-1.871.0821.567796515368153290.5021.20899.7
1.87-20.6742.767257814487144790.7670.75499.9
2-2.160.4274.947057513437134310.910.475100
2.16-2.360.2837.966434212421124120.9590.31699.9
2.36-2.640.18611.695761911195111860.9820.20899.9
2.64-3.050.11317.5853496986698660.9940.126100
3.05-3.730.06225.6541574834783430.9970.07100
3.73-5.270.04435.9634472645164460.9980.04999.9
5.27-62.8080.0373818558356435580.9980.04199.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.761→43.946 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 1952 3.93 %
Rwork0.1818 47663 -
obs0.1828 49615 99.95 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.33 Å2 / Biso mean: 35.1018 Å2 / Biso min: 13.88 Å2
Refinement stepCycle: final / Resolution: 1.761→43.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 146 296 2747
Biso mean--58.68 44.77 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0216730
X-RAY DIFFRACTIONf_angle_d1.99331
X-RAY DIFFRACTIONf_chiral_restr0.266919
X-RAY DIFFRACTIONf_plane_restr0.011327
X-RAY DIFFRACTIONf_dihedral_angle_d19.4942731
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7607-1.80470.31591360.28533233459
1.8047-1.85350.25021370.260433603497
1.8535-1.9080.22991370.226933813518
1.908-1.96960.24211370.210133703507
1.9696-2.040.2641390.20533613500
2.04-2.12170.24671380.196933673505
2.1217-2.21830.22591410.193733973538
2.2183-2.33520.19091370.175833863523
2.3352-2.48150.21771420.172233923534
2.4815-2.67310.17551430.166834003543
2.6731-2.9420.20341410.171534083549
2.942-3.36760.18231380.175634433581
3.3676-4.24230.20441400.163734673607
4.2423-43.95980.19951460.1836083754

+
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