[English] 日本語
Yorodumi
- PDB-1ct8: CATALYTIC ANTIBODY 7C8 COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ct8
TitleCATALYTIC ANTIBODY 7C8 COMPLEX
Components
  • 7C8 FAB FRAGMENT; LONG CHAIN
  • 7C8 FAB FRAGMENT; SHORT CHAIN
KeywordsIMMUNE SYSTEM / ABZYME TRANSITION STATE ANALOG
Function / homology
Function and homology information


humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm
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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-TAA / Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsGigant, B. / Tsumuraya, T. / Fujii, I. / Knossow, M.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Diverse structural solutions to catalysis in a family of antibodies.
Authors: Gigant, B. / Tsumuraya, T. / Fujii, I. / Knossow, M.
History
DepositionAug 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 7C8 FAB FRAGMENT; SHORT CHAIN
B: 7C8 FAB FRAGMENT; LONG CHAIN
C: 7C8 FAB FRAGMENT; SHORT CHAIN
D: 7C8 FAB FRAGMENT; LONG CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8028
Polymers94,4294
Non-polymers1,3734
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 7C8 FAB FRAGMENT; SHORT CHAIN
D: 7C8 FAB FRAGMENT; LONG CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9014
Polymers47,2152
Non-polymers6862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-48 kcal/mol
Surface area18970 Å2
MethodPISA, PQS
3
A: 7C8 FAB FRAGMENT; SHORT CHAIN
B: 7C8 FAB FRAGMENT; LONG CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9014
Polymers47,2152
Non-polymers6862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-48 kcal/mol
Surface area18940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.558, 65.612, 117.761
Angle α, β, γ (deg.)90.00, 95.56, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody 7C8 FAB FRAGMENT; SHORT CHAIN


Mass: 23546.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#2: Antibody 7C8 FAB FRAGMENT; LONG CHAIN


Mass: 23668.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TAA / [4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]-PHOSPHONIC ACID MONO-[2-(2,2-DICHLORO-1-HYDROXY-ETHYLAMINO)-3-HYDROXY-1-(4-NITRO-PHENYL)-PROPYL] ESTER


Mass: 590.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21Cl2F3N3O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 291 K / Method: hanging drop vapor diffusion; seeding used / pH: 4
Details: 30% (w/V) PEG 8000 200mM Ammonium sulfate, pH 4.0, hanging drop vapor diffusion; seeding used, temperature 291K
Crystal grow
*PLUS
pH: 4 / Method: unknown / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlFab11
2150 mM11NaCl
322-26 %(w/v)PEG100012
40.2 Mammonium sulfate12

-
Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 8, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→14.3 Å / Num. all: 40238 / Num. obs: 40238 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.44 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.253 / % possible all: 95.7
Reflection
*PLUS
Num. measured all: 98277
Reflection shell
*PLUS
% possible obs: 95.7 % / Mean I/σ(I) obs: 5.4

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementResolution: 2.2→14.3 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.275 2034 random
Rwork0.211 --
obs-39941 -
Refinement stepCycle: LAST / Resolution: 2.2→14.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 84 195 6921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.75
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 14.3 Å / σ(F): 2 / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / Rfactor obs: 0.3

+
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