[English] 日本語
Yorodumi
- PDB-1qyg: ANTI-COCAINE ANTIBODY M82G2 COMPLEXED WITH BENZOYLECGONINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qyg
TitleANTI-COCAINE ANTIBODY M82G2 COMPLEXED WITH BENZOYLECGONINE
Components
  • FAB M82G2, HEAVY CHAIN
  • FAB M82G2, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ANTI-COCAINE ANTIBODY / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-BCG
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsPozharski, E. / Hewagama, A. / Shanafelt, A. / Petsko, G. / Ringe, D.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Diversity in hapten recognition: structural study of an anti-cocaine antibody M82G2.
Authors: Pozharski, E. / Moulin, A. / Hewagama, A. / Shanafelt, A.B. / Petsko, G.A. / Ringe, D.
History
DepositionSep 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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 No database reference sequence was found for both proteins in this structure at the time ...SEQUENCE No database reference sequence was found for both proteins in this structure at the time of processing

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: FAB M82G2, LIGHT CHAIN
H: FAB M82G2, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6933
Polymers47,4042
Non-polymers2891
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-23 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.170, 75.170, 151.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11L-224-

HOH

21H-540-

HOH

-
Components

#1: Antibody FAB M82G2, LIGHT CHAIN


Mass: 23884.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody FAB M82G2, HEAVY CHAIN


Mass: 23519.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-BCG / 3-(BENZOYLOXY)-8-METHYL-8-AZABICYCLO[3.2.1]OCTANE-2-CARBOXYLIC ACID / BENZOYLECGONINE


Mass: 289.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2M ammonium sulfate, 5% iso-propanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.81→30 Å / Num. all: 38660 / Num. obs: 38660 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.52 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.3
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 4.08 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.89 / % possible all: 75.2

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AR3 (CONSTANT DOMAIN) + PDB ENTRY 1AXT (VARIABLE DOMAIN)

1ar3
PDB Unreleased entry

1axt


Resolution: 1.81→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: BULK SOLVENT MASK CORRECTED TO EXCLUDE INTERNAL CAVITIES
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1935 4.1 %RANDOM
Rwork0.178 ---
all0.189 38660 --
obs0.178 38660 84.4 %-
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.925 Å20.2 Å20 Å2
2---0.925 Å20 Å2
3---1.849 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 21 333 3669
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.033
X-RAY DIFFRACTIONc_angle_deg2.61
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_improper_angle_d1.95
X-RAY DIFFRACTIONc_mcbond_it2.161.5
X-RAY DIFFRACTIONc_mcangle_it2.992
X-RAY DIFFRACTIONc_scbond_it3.32
X-RAY DIFFRACTIONc_scangle_it4.462.5
LS refinement shellResolution: 1.81→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.301 158 3.52 %
Rwork0.2291 3209 -
obs-3209 71.44 %

+
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