[English] 日本語
Yorodumi
- PDB-1a4j: DIELS ALDER CATALYTIC ANTIBODY GERMLINE PRECURSOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a4j
TitleDIELS ALDER CATALYTIC ANTIBODY GERMLINE PRECURSOR
Components
  • IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)
  • IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / ANTIBODY / CATALYTIC ANTIBODY / DIELS ALDER / GERMLINE
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / 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 / B cell receptor signaling pathway / 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 space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSpiller, B.W. / Romesburg, F.E. / Schultz, P.G. / Stevens, R.C.
CitationJournal: Science / Year: 1998
Title: Immunological origins of binding and catalysis in a Diels-Alderase antibody.
Authors: Romesberg, F.E. / Spiller, B. / Schultz, P.G. / Stevens, R.C.
History
DepositionJan 30, 1998Processing site: BNL
Revision 1.0May 13, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)
H: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)
A: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)
B: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)94,6004
Polymers94,6004
Non-polymers00
Water4,756264
1
L: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)
H: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,3002
Polymers47,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-20 kcal/mol
Surface area20290 Å2
MethodPISA
2
A: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)
B: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,3002
Polymers47,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-20 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.900, 49.330, 145.000
Angle α, β, γ (deg.)90.00, 108.74, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)


Mass: 23706.475 Da / Num. of mol.: 2 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 25F2 / Plasmid: P4XH / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: UniProt: P01834
#2: Antibody IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)


Mass: 23593.459 Da / Num. of mol.: 2 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 25F2 / Plasmid: P4XH / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.84 Å3/Da / Density % sol: 51.3 %
Crystal growpH: 6
Details: 19% PEG 8K, 20% GLYCEROL, 200MM MG(CH3COO)2, 10MM CDS04 100MM BISTRIS PH 6.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
210 mMTris-HCl1drop
3100 mM1dropNaCl
41 mMmethionine1drop
519 %PEG1reservoir
620 %glycerol1reservoir
7200 mMmagnesium acetate1reservoir
8100 mMBis-Tris1reservoir
910 mM1reservoirCdSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: WIGGLER
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 63217 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.044 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.27 / % possible all: 95.4
Reflection
*PLUS
Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 95.4 % / Rmerge(I) obs: 0.27

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4K

1a4k


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.292 4197 10 %RANDOM
Rwork0.229 ---
obs0.229 49380 98.5 %-
Displacement parametersBiso mean: 36.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 2 274 7178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.383
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.749
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.355 473 10 %
Rwork0.245 4049 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PR
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.749
LS refinement shell
*PLUS
Rfactor obs: 0.245

+
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