[English] 日本語
Yorodumi
- PDB-2a6d: Crystal structure analysis of the anti-arsonate germline antibody... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a6d
TitleCrystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a phage display derived dodecapeptide RLLIADPPSPRE
Components
  • Dodecapeptide, RLLIADPPSPRE
  • Germline antibody 36-65 Fab Heavy chain
  • Germline antibody 36-65 Fab light chain
KeywordsIMMUNE SYSTEM / Germline / FAB / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSethi, D.K. / Agarwal, A. / Manivel, V. / Rao, K.V. / Salunke, D.M.
CitationJournal: Immunity / Year: 2006
Title: Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response.
Authors: Sethi, D.K. / Agarwal, A. / Manivel, V. / Rao, K.V. / Salunke, D.M.
History
DepositionJul 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE SEQUENCE IS NOT DEPOSITED IN ANY SEQUENCE DATABASE EXCEPT RESIDUES 1 TO 120 OF CHAINS ...SEQUENCE THE SEQUENCE IS NOT DEPOSITED IN ANY SEQUENCE DATABASE EXCEPT RESIDUES 1 TO 120 OF CHAINS B,H WHICH CORRESPOND TO DEPOSITED SEQUENCE OF THE HEAVY CHAIN VARIABLE REGION OF ANTI-ARSONATE ANTIBODY 36-65

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Germline antibody 36-65 Fab light chain
H: Germline antibody 36-65 Fab Heavy chain
A: Germline antibody 36-65 Fab light chain
B: Germline antibody 36-65 Fab Heavy chain
P: Dodecapeptide, RLLIADPPSPRE


Theoretical massNumber of molelcules
Total (without water)96,6655
Polymers96,6655
Non-polymers00
Water1,40578
1
L: Germline antibody 36-65 Fab light chain
H: Germline antibody 36-65 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6502
Polymers47,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-27 kcal/mol
Surface area19820 Å2
MethodPISA
2
A: Germline antibody 36-65 Fab light chain
B: Germline antibody 36-65 Fab Heavy chain
P: Dodecapeptide, RLLIADPPSPRE


Theoretical massNumber of molelcules
Total (without water)49,0153
Polymers49,0153
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.302, 145.670, 71.347
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Germline antibody 36-65 Fab light chain


Mass: 23707.049 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Details: Mouse monoclonal / Source: (natural) Mus musculus (house mouse) / Strain: A/J
#2: Antibody Germline antibody 36-65 Fab Heavy chain


Mass: 23942.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Mouse monoclonal / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Dodecapeptide, RLLIADPPSPRE


Mass: 1365.578 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: chemically synthesized (Phage display derived peptide)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 53.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 18% PEG 8000, cacodylate, 0.05% azide, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2003 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 23421 / Num. obs: 23421 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.87

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FAB

6fab


Resolution: 2.9→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1787 -RANDOM
Rwork0.23 ---
all0.232 23395 --
obs0.232 18109 77.4 %-
Refinement stepCycle: LAST / Resolution: 2.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 0 78 6792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.83949
X-RAY DIFFRACTIONc_bond_d0.012067

+
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