[English] 日本語
Yorodumi
- PDB-4q97: IgNAR antibody domain C1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q97
TitleIgNAR antibody domain C1
ComponentsNovel antigen receptor
KeywordsIMMUNE SYSTEM / protein evolution / antibody structure / protein folding
Function / homology
Function and homology information


Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Novel antigen receptor
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFeige, J.M. / Graewert, M.A. / Marcinowski, M. / Hennig, J. / Behnke, J. / Auslaender, D. / Herold, E.M. / Peschek, J. / Castro, C.D. / Flajnik, M.F. ...Feige, J.M. / Graewert, M.A. / Marcinowski, M. / Hennig, J. / Behnke, J. / Auslaender, D. / Herold, E.M. / Peschek, J. / Castro, C.D. / Flajnik, M.F. / Hendershot, L.M. / Sattler, M. / Groll, M. / Buchner, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins.
Authors: Feige, M.J. / Grawert, M.A. / Marcinowski, M. / Hennig, J. / Behnke, J. / Auslander, D. / Herold, E.M. / Peschek, J. / Castro, C.D. / Flajnik, M. / Hendershot, L.M. / Sattler, M. / Groll, M. / Buchner, J.
History
DepositionApr 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Novel antigen receptor
B: Novel antigen receptor


Theoretical massNumber of molelcules
Total (without water)24,2052
Polymers24,2052
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-16 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.250, 41.250, 98.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 1000
2111B1 - 1000

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999995, 0.002885, -0.000963), (0.002886, -0.999995, 0.001453), (-0.000958, -0.001456, -0.999999)-0.22491, 142.86618, -32.58533

-
Components

#1: Protein Novel antigen receptor / IgNAR antibody


Mass: 12102.545 Da / Num. of mol.: 2 / Fragment: C1 domain (UNP residues 137-243)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q90544
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 M tri-sodium citrate; 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2009
RadiationMonochromator: LN2 cooled fixed-exit double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 7313 / Num. obs: 7190 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.7
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.5 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IND

1ind


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.907 / SU B: 29.129 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28389 360 5 %RANDOM
Rwork0.26538 ---
obs0.26634 6830 98.43 %-
all-7190 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.378 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.79 Å20 Å2
2--0.79 Å20 Å2
3----2.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 0 41 1703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191702
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9432316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09923.63666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.89415284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4281510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211264
X-RAY DIFFRACTIONr_rigid_bond_restr1.40231702
X-RAY DIFFRACTIONr_sphericity_free33.006519
X-RAY DIFFRACTIONr_sphericity_bonded9.58751684
Refine LS restraints NCSNumber: 831 / Type: TIGHT THERMAL / Rms dev position: 2.12 Å / Weight position: 0.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 26 -
Rwork0.361 499 -
obs--98.68 %
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)
10.4580.44730.74830.50230.63933.0898-0.00060.0247-0.0775-0.03590.0917-0.10710.1123-0.0412-0.09110.0993-0.01840.00180.0675-0.02880.034516.775563.6846-13.4919
20.4564-0.4542-0.4210.60640.06691.20880.0303-0.05320.05320.01650.0636-0.0369-0.16760.0415-0.09390.0974-0.00460.01170.0736-0.00850.015116.755579.1984-19.224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 241
2X-RAY DIFFRACTION2B134 - 241

+
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