[English] 日本語
Yorodumi
- PDB-1f3d: CATALYTIC ANTIBODY 4B2 IN COMPLEX WITH ITS AMIDINIUM HAPTEN. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f3d
TitleCATALYTIC ANTIBODY 4B2 IN COMPLEX WITH ITS AMIDINIUM HAPTEN.
Components(CATALYTIC ANTIBODY 4B2) x 2
KeywordsIMMUNE SYSTEM / catalytic antibody / amidinium / haptenic charge
Function / homology
Function and homology information


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 ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-TPM / If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsGolinelli-Pimpaneau, B. / Goncalves, O. / Dintinger, T. / Blanchard, D. / Knossow, M. / Tellier, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structural evidence for a programmed general base in the active site of a catalytic antibody.
Authors: Golinelli-Pimpaneau, B. / Goncalves, O. / Dintinger, T. / Blanchard, D. / Knossow, M. / Tellier, C.
#1: Journal: BIOCHEM.J. / Year: 2000
Title: Mechanism of an Antibody-Catalysed Allylic Isomerization.
Authors: Goncalves, O. / Dintinger, T. / Lebreton, J. / Blanchard, D. / Tellier, C.
History
DepositionJun 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 4, 2012Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: CATALYTIC ANTIBODY 4B2
H: CATALYTIC ANTIBODY 4B2
J: CATALYTIC ANTIBODY 4B2
K: CATALYTIC ANTIBODY 4B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5037
Polymers94,9984
Non-polymers5053
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.000, 87.200, 128.800
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody CATALYTIC ANTIBODY 4B2


Mass: 24206.977 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN - FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue fraction: ASCITES FLUID / References: UniProt: A2NHM3*PLUS
#2: Antibody CATALYTIC ANTIBODY 4B2


Mass: 23292.092 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN - FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue fraction: ASCITES FLUID
#3: Chemical ChemComp-TPM / 2-(4-AMINOBENZYLAMINO)-3,4,5,6-TETRAHYDROPYRIDINIUM


Mass: 204.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, ammonium sulfate, acetate, stontium chloride, glycerol, dioxan, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %(v/v)PEG40001reservoir
23 %(v/v)dioxane1reservoir
320 %(v/v)glycerol1reservoir
40.2 Mammonium sulfate1reservoir
55 mMstrontium chloride1reservoir
620 mMsodium acetate1reservoir
70.25 mMhapten1drop
811.6 mg/mlFab1drop
90.15 M1dropNaCl
100.05 %1dropNaN3

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9607
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9607 Å / Relative weight: 1
ReflectionResolution: 1.87→20 Å / Num. all: 81391 / Num. obs: 79647 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 1.84 % / Biso Wilson estimate: 24.15 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3755 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 155936
Reflection shell
*PLUS
% possible obs: 94.9 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 7975 -RANDOM
Rwork0.198 ---
all-79627 --
obs-79342 97.5 %-
Refinement stepCycle: LAST / Resolution: 1.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6600 0 35 308 6943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.411
X-RAY DIFFRACTIONc_bond_d0.006
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.87 Å / Lowest resolution: 1.9 Å / Rfactor Rfree: 0.281 / Rfactor obs: 0.274

+
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