[English] 日本語
Yorodumi
- PDB-2a6k: Crystal Structure Analysis of the germline antibody 36-65 Fab in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a6k
TitleCrystal Structure Analysis of the germline antibody 36-65 Fab in complex with the dodecapeptide SLGDNLTNHNLR
Components
  • DODECAPEPTIDE: SLGDNLTNHNLR
  • Germline antibody 36-65 Fab heavy chain
  • Germline antibody 36-65 Fab light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Fab-peptide complex
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin / Immunoglobulin subtype / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin / Immunoglobulin subtype / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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 3, 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 21, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
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
A: Germline antibody 36-65 Fab light chain
B: Germline antibody 36-65 Fab heavy chain
L: Germline antibody 36-65 Fab light chain
H: Germline antibody 36-65 Fab heavy chain
P: DODECAPEPTIDE: SLGDNLTNHNLR


Theoretical massNumber of molelcules
Total (without water)96,6555
Polymers96,6555
Non-polymers00
Water1,856103
1
A: Germline antibody 36-65 Fab light chain
B: 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 area3770 Å2
ΔGint-25 kcal/mol
Surface area19760 Å2
MethodPISA
2
L: Germline antibody 36-65 Fab light chain
H: Germline antibody 36-65 Fab heavy chain
P: DODECAPEPTIDE: SLGDNLTNHNLR


Theoretical massNumber of molelcules
Total (without water)49,0053
Polymers49,0053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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 area3630 Å2
ΔGint-26 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)53.135, 144.920, 70.991
Angle α, β, γ (deg.)90.00, 104.35, 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)
#2: Antibody Germline antibody 36-65 Fab heavy chain


Mass: 23942.768 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Details: mouse monoclonal / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6PF95
#3: Protein/peptide DODECAPEPTIDE: SLGDNLTNHNLR


Mass: 1355.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized peptide
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20% PEG 8000, cacodylate, 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: Aug 10, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 19662 / Num. obs: 19662 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.04 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 4
Reflection shellResolution: 3→3.11 Å / % possible all: 95.9

-
Processing

Software
NameVersionClassification
MAR345data collection
AUTOMARdata reduction
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1813 8.7 %random
Rwork0.245 ---
all0.246 20866 --
obs0.246 18490 88.6 %-
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6661 0 0 103 6764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.73493
X-RAY DIFFRACTIONc_bond_d0.01013

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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