[English] 日本語
Yorodumi
- PDB-1igj: 26-10 FAB:DIGOXIN COMPLEX-AFFINITY AND SPECIFICITY DUE TO SURFACE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1igj
Title26-10 FAB:DIGOXIN COMPLEX-AFFINITY AND SPECIFICITY DUE TO SURFACE COMPLEMENTARITY
Components
  • IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DIGOXIN / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsJeffrey, P.D. / Sheriff, S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: 26-10 Fab-digoxin complex: affinity and specificity due to surface complementarity.
Authors: Jeffrey, P.D. / Strong, R.K. / Sieker, L.C. / Chang, C.Y. / Campbell, R.L. / Petsko, G.A. / Haber, E. / Margolies, M.N. / Sheriff, S.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Crystallization of the Fab Fragment of a Monoclonal Anti-Digoxin Antibody and its Complex with Digoxin
Authors: Rose, D.R. / Seaton, B.A. / Petsko, G.A. / Novotny, J. / Margolies, M.N. / Locke, E. / Haber, E.
#2: Journal: Acta Crystallogr.,Sect.A / Year: 1991
Title: Solution of a Fab (26-10)Digoxin Complex by Generalized Molecular Replacement
Authors: Brunger, A.T.
History
DepositionFeb 19, 1993Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
B: IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
C: IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
D: IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2916
Polymers94,7294
Non-polymers1,5622
Water00
1
A: IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
B: IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1463
Polymers47,3652
Non-polymers7811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-27 kcal/mol
Surface area19050 Å2
MethodPISA
2
C: IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)
D: IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1463
Polymers47,3652
Non-polymers7811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-29 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.160, 164.430, 70.010
Angle α, β, γ (deg.)90.00, 108.37, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 8, 95, 141 OF THE A AND C CHAINS AND 149, 151, 200 OF THE B AND D CHAINS ARE CIS PROLINES.

-
Components

#1: Antibody IGG2A-KAPPA 26-10 FAB (LIGHT CHAIN)


Mass: 24057.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: S52028
#2: Antibody IGG2A-KAPPA 26-10 FAB (HEAVY CHAIN)


Mass: 23307.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: S38950
#3: Chemical ChemComp-DGX / DIGOXIN


Mass: 780.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H64O14
Has protein modificationY
Nonpolymer detailsDIGOXIN IS DIGOXIGENIN TRIDIGITOXOSIDE, HOWEVER, THERE IS NO ELECTRON DENSITY FOR THE OUTERMOST TWO ...DIGOXIN IS DIGOXIGENIN TRIDIGITOXOSIDE, HOWEVER, THERE IS NO ELECTRON DENSITY FOR THE OUTERMOST TWO DIGITOXOSES IN BOTH COMPLEXES.
Sequence detailsTHE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT,T.T.WU,H.M.PERRY,K.S. ...THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT,T.T.WU,H.M.PERRY,K.S.GOTTESMAN,C.FOELLER SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED., (1991), NATIONAL INSTITUTES OF HEALTH,BETHESDA,MD.).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116-18 %(w/w)PEG800011
21.7 %(v/v)MPD11
310 mMsodium phosphate11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 27121 / Num. measured all: 68345 / Rmerge(I) obs: 0.048

-
Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→8 Å / Rfactor Rwork: 0.176 / σ(F): 1
Details: CRYSTALS ARE TWINNED BY HEMI-MEROHEDRY SUCH THAT (H,K,L) REFLECTIONS FROM ONE LATTICE AND (H,K,-H-L) REFLECTIONS FROM THE OTHER LATTICE ARE SPATIALLY OVERLAPPED. TWIN FRACTION FOR CRYSTAL ...Details: CRYSTALS ARE TWINNED BY HEMI-MEROHEDRY SUCH THAT (H,K,L) REFLECTIONS FROM ONE LATTICE AND (H,K,-H-L) REFLECTIONS FROM THE OTHER LATTICE ARE SPATIALLY OVERLAPPED. TWIN FRACTION FOR CRYSTAL WHOSE DATA THE MODEL WAS REFINED AGAINST WAS ESTIMATED AT 43%. THE FOLLOWING REGIONS OF THE HEAVY CHAINS (B AND D) WERE INCLUDED IN THE MODEL BUT HAVE POORLY DEFINED ELECTRON DENSITY: 25 - 31, 53 - 56, AND 127 - 137.
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 74 0 6652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_dihedral_angle_d28.1
X-RAY DIFFRACTIONx_improper_angle_d1.39
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 25135 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

+
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