[English] 日本語
Yorodumi
- PDB-7mrq: Chicken CNTN4 FN1-FN3 domains with T751A, V752A, Y781A, E786A mut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mrq
TitleChicken CNTN4 FN1-FN3 domains with T751A, V752A, Y781A, E786A mutations
ComponentsContactin-4
KeywordsCELL ADHESION / Ig superfamily
Function / homology
Function and homology information


axon guidance / cell adhesion / plasma membrane
Similarity search - Function
Basigin-like / Immunoglobulin I-set / Immunoglobulin I-set domain / 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 ...Basigin-like / Immunoglobulin I-set / Immunoglobulin I-set domain / 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
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBouyain, S. / Karuppan, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R15NS108371-01 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Members of the vertebrate contactin and amyloid precursor protein families interact through a conserved interface.
Authors: Karuppan, S.J. / Vogt, A. / Fischer, Z. / Ladutska, A. / Swiastyn, J. / McGraw, H.F. / Bouyain, S.
History
DepositionMay 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Contactin-4


Theoretical massNumber of molelcules
Total (without water)33,3501
Polymers33,3501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.010, 91.460, 124.290
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 Contactin-4


Mass: 33350.027 Da / Num. of mol.: 1 / Fragment: FN1-FN3 domains / Mutation: T751A, V752A, Y781A, E786A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CNTN4 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: F1P3U6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.03 Å3/Da / Density % sol: 79.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4.2M NaCl, 2 (v/v) % Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 13597 / % possible obs: 95.1 % / Redundancy: 11.3 % / Biso Wilson estimate: 103.76 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.193 / Rrim(I) all: 0.202 / Net I/σ(I): 12
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1014 / CC1/2: 0.846 / Rrim(I) all: 0.812 / % possible all: 71.7

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E4S

5e4s


Resolution: 3.2→46.77 Å / SU ML: 0.4601 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.6697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 1350 10.06 %
Rwork0.2209 12065 -
obs0.225 13415 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.56 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 0 0 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552332
X-RAY DIFFRACTIONf_angle_d0.81963192
X-RAY DIFFRACTIONf_chiral_restr0.0551358
X-RAY DIFFRACTIONf_plane_restr0.0068420
X-RAY DIFFRACTIONf_dihedral_angle_d12.469846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.310.43731130.3511973X-RAY DIFFRACTION80.38
3.31-3.450.40471220.33121098X-RAY DIFFRACTION89.57
3.45-3.60.31911330.29411177X-RAY DIFFRACTION95.97
3.6-3.790.27191360.23991226X-RAY DIFFRACTION99.71
3.79-4.030.26751380.21911235X-RAY DIFFRACTION99.93
4.03-4.340.25971380.21121233X-RAY DIFFRACTION99.93
4.34-4.780.23161390.17611248X-RAY DIFFRACTION99.78
4.78-5.470.19841410.16771265X-RAY DIFFRACTION100
5.47-6.890.24241400.21251260X-RAY DIFFRACTION100
6.89-46.770.26241500.22721350X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.48842137447-1.601907529942.284969210377.12237894506-1.507406657674.961352263270.8136466545260.204131524719-1.74596894163-0.754598571546-0.02918027642640.2549919139431.85179721120.327761448893-0.7624693211551.979039596160.00356226582333-0.3140452445890.666523602901-0.04752217790691.1446053788622.7165653589-47.81096292324.3052667978
27.75827068099-3.80761395041.850385130099.27629147125-2.77078499796.845233378550.468585623490.06991179789180.4096103147080.622980796754-0.221362465291-0.0387867117807-0.4848470388660.136963993716-0.2908138322161.29453727228-0.1756240388120.02661871855180.6227034629330.001865333392640.6828026801252.83773466502-17.5831364525-15.2744853862
38.178571556784.18229536114-2.135785590164.92351329514-4.625047410929.38979245506-0.0968522073409-0.370306188808-0.679423746743-0.508504319723-0.752532241238-1.306589978870.5033858782930.7530785593520.885341828181.372239409860.196064628130.09846006966860.7122506341240.1692979106640.93379038157111.073013956915.5718709264-40.5642946398
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 598 through 697 )598 - 6971 - 100
22chain 'A' and (resid 698 through 799 )698 - 799101 - 202
33chain 'A' and (resid 800 through 900 )800 - 900203 - 297

+
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