[English] 日本語
Yorodumi
- PDB-2imn: Refined crystal structure of a recombinant immunoglobulin domain ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2imn
TitleRefined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant
ComponentsIGA-KAPPA MCPC603 FV (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.97 Å
AuthorsSteipe, B. / Huber, R.
CitationJournal: J.Mol.Biol. / Year: 1992
Title: Refined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant.
Authors: Steipe, B. / Pluckthun, A. / Huber, R.
History
DepositionMar 30, 1992-
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4613
Polymers12,3061
Non-polymers1552
Water2,162120
1
A: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules

A: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9226
Polymers24,6122
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
Buried area1980 Å2
ΔGint-23 kcal/mol
Surface area11010 Å2
MethodPISA, PQS
2
A: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules

A: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9226
Polymers24,6122
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area1170 Å2
ΔGint-40 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.500, 86.500, 74.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Atom site foot note1: RESIDUES PRO 8 AND PRO 95 ARE CIS-PROLINES.
2: RESIDUES TYR 31, LYS 31A, LYS 103, AND ARG 108 ARE PARTIALLY DISORDERED IN THE ELECTRON DENSITY.

-
Components

#1: Antibody IGA-KAPPA MCPC603 FV (LIGHT CHAIN)


Mass: 12305.757 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 208622
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.41 %

-
Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 11262 / Num. measured all: 96963 / Rmerge(I) obs: 0.086

-
Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.149 / Highest resolution: 1.97 Å
Details: RESIDUES TYR 31, LYS 31A, LYS 103, AND ARG 108 ARE PARTIALLY DISORDERED IN THE ELECTRON DENSITY.
Refinement stepCycle: LAST / Highest resolution: 1.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 9 120 993
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.23
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 1.97 Å / Rfactor obs: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.23

+
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