[English] 日本語
Yorodumi
- PDB-2i27: Crystal Structure Analysis of the Nurse Shark New Antigen Recepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i27
TitleCrystal Structure Analysis of the Nurse Shark New Antigen Receptor Ancestral variable domain
ComponentsNew Antigen Receptor Ancestral
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homology
Function and homology information


T cell receptor complex / peptide antigen binding / adaptive immune response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
Biological speciesGinglymostoma cirratum (nurse shark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsStanfield, R.L. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Maturation of Shark Single-domain (IgNAR) Antibodies: Evidence for Induced-fit Binding.
Authors: Stanfield, R.L. / Dooley, H. / Verdino, P. / Flajnik, M.F. / Wilson, I.A.
History
DepositionAug 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR THE NEW ANTIGEN ...SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR THE NEW ANTIGEN RECEPTOR ANCESTRAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
N: New Antigen Receptor Ancestral
O: New Antigen Receptor Ancestral


Theoretical massNumber of molelcules
Total (without water)26,5892
Polymers26,5892
Non-polymers00
Water1,45981
1
N: New Antigen Receptor Ancestral


Theoretical massNumber of molelcules
Total (without water)13,2941
Polymers13,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: New Antigen Receptor Ancestral


Theoretical massNumber of molelcules
Total (without water)13,2941
Polymers13,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.423, 61.398, 103.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein New Antigen Receptor Ancestral


Mass: 13294.453 Da / Num. of mol.: 2 / Fragment: variable domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Plasmid: pims100 / Production host: Escherichia coli (E. coli) / Strain (production host): xl1-blue / References: UniProt: Q8JGJ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 26% PEG 4000, 0.1M hepes, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979454 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979454 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 15147 / Num. obs: 15147 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.09 / Net I/σ(I): 33.7
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 5075 / Rsym value: 0.664 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.164 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.204 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28052 730 4.8 %RANDOM
Rwork0.21692 ---
obs0.21996 14355 99.77 %-
all-14355 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.49 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 0 81 1730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211667
X-RAY DIFFRACTIONr_bond_other_d0.0090.021126
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9532251
X-RAY DIFFRACTIONr_angle_other_deg0.9453.0032737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9755213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04424.47476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91715290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2171514
X-RAY DIFFRACTIONr_chiral_restr0.1050.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
X-RAY DIFFRACTIONr_nbd_refined0.2450.2282
X-RAY DIFFRACTIONr_nbd_other0.2220.21157
X-RAY DIFFRACTIONr_nbtor_refined0.180.2794
X-RAY DIFFRACTIONr_nbtor_other0.090.21017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3320.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2991.51406
X-RAY DIFFRACTIONr_mcbond_other0.2951.5446
X-RAY DIFFRACTIONr_mcangle_it1.66121719
X-RAY DIFFRACTIONr_scbond_it2.6793759
X-RAY DIFFRACTIONr_scangle_it3.2394.5532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 61 -
Rwork0.276 1044 -
obs-1044 100 %
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)
12.7667-1.0994-0.50454.9611-0.63094.3332-0.08430.15780.18810.16470.0213-0.3333-0.0827-0.00760.0629-0.2314-0.0435-0.0074-0.1661-0.0141-0.135335.524930.820939.8101
25.57821.91081.95053.86742.64026.51890.29650.05360.22350.4869-0.1696-0.10130.4356-0.0298-0.1269-0.1193-0.05370.0149-0.20340.0105-0.163330.26366.015438.0917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1NA2 - 1142 - 114
2X-RAY DIFFRACTION2OB2 - 1132 - 113

+
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