[English] 日本語
Yorodumi
- PDB-1j05: The crystal structure of anti-carcinoembryonic antigen monoclonal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j05
TitleThe crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment
Components
  • anti-CEA mAb T84.66, heavy chain
  • anti-CEA mAb T84.66, light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular region
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 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
PHOSPHATE ION / Ig kappa chain V-III region PC 3741/TEPC 111 / Anti-myosin immunoglobulin heavy chain variable region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKondo, H. / Nishimura, Y. / Shiroishi, M. / Asano, R. / Noro, N. / Tsumoto, K. / Kumagai, I.
CitationJournal: To be Published
Title: The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment
Authors: Kondo, H. / Nishimura, Y. / Shiroishi, M. / Asano, R. / Noro, N. / Tsumoto, K. / Kumagai, I.
History
DepositionNov 1, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: anti-CEA mAb T84.66, light chain
H: anti-CEA mAb T84.66, heavy chain
A: anti-CEA mAb T84.66, light chain
B: anti-CEA mAb T84.66, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0688
Polymers50,6944
Non-polymers3744
Water4,612256
1
L: anti-CEA mAb T84.66, light chain
H: anti-CEA mAb T84.66, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5344
Polymers25,3472
Non-polymers1872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-17 kcal/mol
Surface area10600 Å2
MethodPISA
2
A: anti-CEA mAb T84.66, light chain
B: anti-CEA mAb T84.66, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5344
Polymers25,3472
Non-polymers1872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-17 kcal/mol
Surface area10410 Å2
MethodPISA
3
A: anti-CEA mAb T84.66, light chain
B: anti-CEA mAb T84.66, heavy chain
hetero molecules

L: anti-CEA mAb T84.66, light chain
H: anti-CEA mAb T84.66, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0688
Polymers50,6944
Non-polymers3744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area5150 Å2
ΔGint-39 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.774, 75.033, 63.105
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assemblies are formed between chain L and H and between A and B.

-
Components

#1: Antibody anti-CEA mAb T84.66, light chain / T84.66 antibody


Mass: 12113.562 Da / Num. of mol.: 2 / Fragment: Fv fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01660
#2: Antibody anti-CEA mAb T84.66, heavy chain / T84.66 antibody


Mass: 13233.598 Da / Num. of mol.: 2 / Fragment: Fv fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JL85
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.7 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na, K Phosphate, Na Hepes, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→23.25 Å / Num. all: 91647 / Num. obs: 91647 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 6.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.2 / Num. unique all: 13262 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
SHELXL-97refinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→5 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.217 8909 random
Rwork0.185 --
all0.19 91647 -
obs0.185 88978 -
Refinement stepCycle: LAST / Resolution: 1.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 22 256 3840

+
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