[English] 日本語
Yorodumi
- PDB-2ajz: Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ajz
TitleCrystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with ecgonine methyl ester
Components(Antibody 7A1 Fab') x 2
KeywordsIMMUNE SYSTEM / catalytic Antibody / Fab / ecgonine methyl ester / HYDROLYTIC
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / B cell differentiation / antigen binding / blood microparticle / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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
Chem-ECG / Vh gene product / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: Structure / Year: 2006
Title: Complete reaction cycle of a cocaine catalytic antibody at atomic resolution.
Authors: Zhu, X. / Dickerson, T.J. / Rogers, C.J. / Kaufmann, G.F. / Mee, J.M. / McKenzie, K.M. / Janda, K.D. / Wilson, I.A.
History
DepositionAug 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 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 1.4Aug 23, 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
Remark 999SEQUENCE The sequence of these proteins are not available at any sequence database at the time of processing.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Antibody 7A1 Fab'
H: Antibody 7A1 Fab'
A: Antibody 7A1 Fab'
B: Antibody 7A1 Fab'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2496
Polymers95,8514
Non-polymers3982
Water4,738263
1
L: Antibody 7A1 Fab'
H: Antibody 7A1 Fab'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1253
Polymers47,9252
Non-polymers1991
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-21 kcal/mol
Surface area19850 Å2
MethodPISA
2
A: Antibody 7A1 Fab'
B: Antibody 7A1 Fab'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1253
Polymers47,9252
Non-polymers1991
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-22 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.934, 78.489, 130.334
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Antibody 7A1 Fab'


Mass: 24059.611 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN IGG1 KAPPA LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#2: Antibody Antibody 7A1 Fab'


Mass: 23865.783 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN IGG1 heavy CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NUE8
#3: Chemical ChemComp-ECG / 3-HYDROXY-8-METHYL-8-AZA-BICYCLO[3.2.1]OCTANE-2-CARBOXYLIC ACID METHYL ESTER / ECGONINE METHYL ESTER


Mass: 199.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 52.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 4000, ammonium fluoride, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 8, 2003
RadiationMonochromator: DOUBLE-CRYSTAL, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 40412 / % possible obs: 90.2 % / Rmerge(I) obs: 0.099 / Χ2: 3.303
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 65.2 % / Rmerge(I) obs: 0.363 / Num. measured obs: 2905 / Χ2: 3.576 / % possible all: 65.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
HKL-2000data scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb ENTRY 2AJS

2ajs


Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1878 4.4 %RANDOM
Rwork0.238 ---
obs-37144 86.2 %-
Solvent computationBsol: 60.308 Å2
Displacement parametersBiso mean: 35.657 Å2
Baniso -1Baniso -2Baniso -3
1-6.395 Å20 Å2-5.054 Å2
2--6.203 Å20 Å2
3----12.598 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 28 263 7037
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_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://pdbjlvh1.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