[English] 日本語
Yorodumi
- PDB-6tpv: Crystal structures of FNIII domain one and two of the human leuco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tpv
TitleCrystal structures of FNIII domain one and two of the human leucocyte common antigen-related protein, LAR
ComponentsReceptor-type tyrosine-protein phosphatase F
KeywordsCELL ADHESION / Fibronectin type-III / adhesion protein
Function / homology
Function and homology information


chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity ...chondroitin sulfate proteoglycan binding / cell surface receptor protein tyrosine phosphatase signaling pathway / neuron projection regeneration / Receptor-type tyrosine-protein phosphatases / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / Synaptic adhesion-like molecules / regulation of axon regeneration / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / cell adhesion molecule binding / Insulin receptor recycling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of receptor binding / cell migration / heparin binding / cell adhesion / neuron projection / neuronal cell body / protein-containing complex binding / signal transduction / extracellular exosome / plasma membrane
Similarity search - Function
: / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...: / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Receptor-type tyrosine-protein phosphatase F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVilstrup, J.P. / Thirup, S.S. / Simonsen, A. / Birkefeldt, T. / Strandbygaard, D.
Funding support Denmark, 2items
OrganizationGrant numberCountry
LundbeckfondenR198-2015-168 Denmark
Novo Nordisk FoundationDFF 4183-00604 Denmark
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystal and solution structures of fragments of the human leucocyte common antigen-related protein.
Authors: Vilstrup, J. / Simonsen, A. / Birkefeldt, T. / Strandbygard, D. / Lyngso, J. / Pedersen, J.S. / Thirup, S.
History
DepositionDec 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase F
B: Receptor-type tyrosine-protein phosphatase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5283
Polymers45,4592
Non-polymers691
Water6,125340
1
A: Receptor-type tyrosine-protein phosphatase F


Theoretical massNumber of molelcules
Total (without water)22,7291
Polymers22,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7982
Polymers22,7291
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.270, 50.843, 65.525
Angle α, β, γ (deg.)90.000, 97.220, 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 Receptor-type tyrosine-protein phosphatase F / Leukocyte common antigen related / LAR


Mass: 22729.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRF, LAR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10586, protein-tyrosine-phosphatase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M Sodium citrate tribasic dihydrate pH 8.3, 20 % PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→40.05 Å / Num. obs: 37701 / % possible obs: 97.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 17.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.81 / Num. unique obs: 2761 / CC1/2: 0.888 / Rrim(I) all: 0.98 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIXv1.16-3549-000refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DJU

2dju


Resolution: 1.8→40.05 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.22 --1992
Rwork0.1855 ---
obs-37545 97.44 %-
Displacement parametersBiso mean: 41.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 5 340 3300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01373072
X-RAY DIFFRACTIONf_angle_d1.18254217
X-RAY DIFFRACTIONf_chiral_restr0.0786468
X-RAY DIFFRACTIONf_plane_restr0.0089559
X-RAY DIFFRACTIONf_dihedral_angle_d21.87261849

+
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