[English] 日本語
Yorodumi
- PDB-1ar2: DISULFIDE-FREE IMMUNOGLOBULIN FRAGMENT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ar2
TitleDISULFIDE-FREE IMMUNOGLOBULIN FRAGMENT
ComponentsREI
KeywordsIMMUNOGLOBULIN / DISULFIDE-FREE / IMMUNOGLOBULIN FRAGMENT / BENCE-JONES
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular exosome / extracellular region / plasma membrane
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
Immunoglobulin kappa variable 1D-33 / Immunoglobulin kappa variable 1D-33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsUson, I. / Bes, M.T. / Sheldrick, G.M. / Schneider, T.R. / Hartsch, T. / Fritz, H.-J.
CitationJournal: Structure Fold.Des. / Year: 1997
Title: X-ray crystallography reveals stringent conservation of protein fold after removal of the only disulfide bridge from a stabilized immunoglobulin variable domain.
Authors: Uson, I. / Bes, M.T. / Sheldrick, G.M. / Schneider, T.R. / Hartsch, T. / Fritz, H.J.
History
DepositionAug 8, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Other
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: REI


Theoretical massNumber of molelcules
Total (without water)11,9211
Polymers11,9211
Non-polymers00
Water30617
1
A: REI

A: REI


Theoretical massNumber of molelcules
Total (without water)23,8422
Polymers23,8422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Unit cell
Length a, b, c (Å)52.800, 52.800, 158.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-126-

HOH

-
Components

#1: Antibody REI / IG KAPPA CHAIN V-I REGION


Mass: 11921.168 Da / Num. of mol.: 1 / Fragment: VARIABLE REGION, LIGHT CHAIN / Mutation: INS(TP-1D), C25V, Y34H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01607, UniProt: P01593*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.6
Details: VAPOUR DIFFUSION AL 4 C FROM A PROTEIN SOLUTION CONTAINING 8 MG/ML IN 50 MM POTASSIUM PHOSPHATE BUFFER AL PH 7, USING 2 M AMMONIUM SULFATE IN 100 MM SODIUM ACETATE BUFFER, PH 4.6, vapor ...Details: VAPOUR DIFFUSION AL 4 C FROM A PROTEIN SOLUTION CONTAINING 8 MG/ML IN 50 MM POTASSIUM PHOSPHATE BUFFER AL PH 7, USING 2 M AMMONIUM SULFATE IN 100 MM SODIUM ACETATE BUFFER, PH 4.6, vapor diffusion, temperature 277K
PH range: 4.6-7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
250 mMpotassium phosphate1drop
32 Mammonium sulfate1reservoir
4100 mMsodium acetatex1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.901
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 28, 1996 / Details: BENT CRYSTAL MONOCHROMATOR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 2.8→75 Å / Num. obs: 3549 / % possible obs: 97 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.104 / Rsym value: 0.088 / Net I/σ(I): 11.1
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.43 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 37985
Reflection shell
*PLUS
% possible obs: 97.8 %

-
Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1REI

1rei


Resolution: 2.8→75 Å / Num. parameters: 3434 / Num. restraintsaints: 4775 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: SIMULATED ANNEALING WITH X-PLOR, FINAL REFINEMENT WITH SHELXL-97
RfactorNum. reflection% reflectionSelection details
Rfree0.4152 340 10 %EVERY 10TH REFLECTION
all0.28 3528 --
obs0.2543 -97 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 819 / Occupancy sum non hydrogen: 857.5
Refinement stepCycle: LAST / Resolution: 2.8→75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 0 17 857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.017
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.041
X-RAY DIFFRACTIONs_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.016
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 75 Å / Rfactor all: 0.28 / Rfactor obs: 0.228 / Rfactor Rfree: 0.343 / Rfactor Rwork: 0.2543
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg30.2
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.3

+
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