[English] 日本語
Yorodumi
- PDB-1qbm: FAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qbm
TitleFAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION
Components(E8B ANTIBODY) x 2
KeywordsIMMUNOGLOBULIN / IGG1 KAPPA / ANTIBODY / FAB FRAGMENT / ANTI-CYTOCHROME C ANTIBODY
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response
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-like fold ...: / 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
: / : / Immunoglobulin kappa chain variable 12-41
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsMylvaganam, S.E. / Paterson, Y. / Getzoff, E.D.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution.
Authors: Mylvaganam, S.E. / Paterson, Y. / Getzoff, E.D.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Biochemical Implications from the Variable Gene Sequences of an Anti-Cytochrome C Antibody and Crystallographic Characterization of its Antigen-Binding Fragment in Free and Antigen-Complexed Forms
Authors: Mylvaganam, S.E. / Paterson, Y. / Kaiser, K. / Bowdish, K. / Getzoff, E.D.
#2: Journal: J.Immunol. / Year: 1985
Title: Monoclonal Antibodies to Horse Cytochrome C Expressing Four Distinct Idiotypes Distribute Among Two Sites on the Native Protein
Authors: Carbone, F.R. / Paterson, Y.
History
DepositionMay 1, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
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
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: E8B ANTIBODY
H: E8B ANTIBODY


Theoretical massNumber of molelcules
Total (without water)47,1602
Polymers47,1602
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-25 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.960, 85.010, 63.330
Angle α, β, γ (deg.)90.00, 105.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody E8B ANTIBODY / FAB E8


Mass: 23655.057 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: E8 ANTIBODY PURIFIED FROM ASCITES / Source: (natural) Mus musculus (house mouse) / Cell line: P3-X63-AG8.653 / Organ: SPLEEN / Strain: BALB/C / References: GenBank: 2072141, UniProt: P01635*PLUS
#2: Antibody E8B ANTIBODY / FAB E8


Mass: 23505.213 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: E8 ANTIBODY PURIFIED FROM ASCITES / Source: (natural) Mus musculus (house mouse) / Cell line: P3-X63-AG8.653 / Organ: SPLEEN / Strain: BALB/C / References: PIR: S49220
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.4 / Details: pH 6.4
Crystal grow
*PLUS
pH: 6.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.05 Msodium ammonium phosphate11
220 %(w/v)PEG400011

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.37 Å / Num. obs: 17924 / % possible obs: 91.6 % / Redundancy: 3 % / Biso Wilson estimate: 45.2 Å2 / Rsym value: 0.146 / Net I/σ(I): 14
Reflection shellResolution: 2.37→2.47 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.44 / % possible all: 52.3
Reflection
*PLUS
Rmerge(I) obs: 0.146
Reflection shell
*PLUS
% possible obs: 52.3 % / Rmerge(I) obs: 0.44

-
Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.8model building
X-PLOR3.8refinement
XENGENdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2.26 ANGSTROM RESOLUTION FAB E8A

Resolution: 2.37→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.269 -10 %
Rwork0.194 --
obs0.194 15334 82.8 %
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -3Baniso -2
1--0.464 Å22.374 Å2-
2----2.748 Å2
3--2.749 Å2-
Refine analyze
ObsFree
Luzzati d res low20 Å-
Luzzati sigma a0.41 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.37→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 0 127 3445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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: 2.37→2.48 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4955 -4.1 %
Rwork0.4094 894 -
obs--39.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1
X-RAY DIFFRACTION2PARHCSDXB.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

+
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