[English] 日本語
Yorodumi
- PDB-1zea: Structure of the anti-cholera toxin antibody Fab fragment TE33 in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zea
TitleStructure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide
Components
  • monoclonal anti-cholera toxin IGG1 KAPPA antibody, H chain
  • monoclonal anti-cholera toxin IGG1 KAPPA antibody, L chain
  • short synthetic D-amino acid peptide D2
KeywordsIMMUNE SYSTEM / polyspecificity / cross-reactivity / anti-cholera toxin / antigen-antibody complex / antigen recognition / substitution matrix
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / metal ion binding
Similarity search - Function
: / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site ...: / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / If kappa light chain / Anti-CEA 79 single chain Fv
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsScheerer, P. / Krauss, N. / Wessner, H. / Scholz, C. / Otte, L. / Seifert, M. / Kramer, A. / Schneider-Mergener, J. / Hoehne, W.
CitationJournal: J.Mol.Recognit. / Year: 2007
Title: Structure of an anti-cholera toxin antibody Fab in complex with an epitope-derived D-peptide: a case of polyspecific recognition.
Authors: Scheerer, P. / Kramer, A. / Otte, L. / Seifert, M. / Wessner, H. / Scholz, C. / Krauss, N. / Schneider-Mergener, J. / Hohne, W.
History
DepositionApr 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 28, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / pdbx_entity_src_syn ...diffrn_source / pdbx_entity_src_syn / reflns / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: monoclonal anti-cholera toxin IGG1 KAPPA antibody, L chain
H: monoclonal anti-cholera toxin IGG1 KAPPA antibody, H chain
A: short synthetic D-amino acid peptide D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6285
Polymers48,2443
Non-polymers3842
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.638, 108.862, 40.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Antibody monoclonal anti-cholera toxin IGG1 KAPPA antibody, L chain


Mass: 23843.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Strain: BALB/c / References: UniProt: A2NHM3
#2: Antibody monoclonal anti-cholera toxin IGG1 KAPPA antibody, H chain


Mass: 23410.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Strain: BALB/c / References: UniProt: Q921A6
#3: Protein/peptide short synthetic D-amino acid peptide D2


Mass: 990.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This D-amino acid sequence occurs peptide synthesis
Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.33 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 8000, citrat buffer, potassium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8095 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2001 / Details: bent mirrors
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8095 Å / Relative weight: 1
ReflectionResolution: 1.78→23 Å / Num. all: 40461 / Num. obs: 40461 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.78 % / Biso Wilson estimate: 20.25 Å2 / Rsym value: 0.064 / Net I/σ(I): 14.14
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.29 % / Mean I/σ(I) obs: 3.27 / Num. unique all: 1916 / Rsym value: 0.317 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TET

1tet


Resolution: 1.78→23 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The current model includes the FAB fragment TE33, residues DVA A 1 - DSN A 9 of the bound D-amino acid peptide D2, 276 water molecules and 2 CITRATE ion. The light and heavy chains have been ...Details: The current model includes the FAB fragment TE33, residues DVA A 1 - DSN A 9 of the bound D-amino acid peptide D2, 276 water molecules and 2 CITRATE ion. The light and heavy chains have been designated *L* and *H*, respectively. Peptide has been designated *A*. The numbering of TE33 residues is essentially according to E. KABAT (E.A. KABAT,T.T. WU, H.M. PERRY, K.S. GOTTESMAN, sequences of proteins of Imuunological interest, 5TH ED.,(1991), NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD.). There is no electron density corresponding to the 7-residue stretch H 127 - H 133 in the constant domain of heavy chain H.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1989 -random
Rwork0.198 ---
all0.201 40407 --
obs0.201 40407 93.4 %-
Displacement parametersBiso mean: 23.0271 Å2
Baniso -1Baniso -2Baniso -3
1--2.057 Å20 Å20 Å2
2--0.188 Å20 Å2
3---1.868 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.09 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.78→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 26 276 3656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0119
X-RAY DIFFRACTIONc_angle_deg1.91236
X-RAY DIFFRACTIONc_dihedral_angle_deg28.06804
X-RAY DIFFRACTIONc_improper_angle_d1.94903
LS refinement shellResolution: 1.78→1.84 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.261 172 -
Rwork0.217 --
obs-3796 85.05 %

+
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