[English] 日本語
Yorodumi
- PDB-8fzp: Crystal structure of polyreactive 43G10 mouse Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fzp
TitleCrystal structure of polyreactive 43G10 mouse Fab
Components
  • 43G10 Fab heavy chain
  • 43G10 Fab light chain
KeywordsIMMUNE SYSTEM / Polyreactivity / Polyspecificity / Fab / Immunoglobulin A
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsBorowska, M.T. / Adams, E.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI147954 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI115471 United States
CitationJournal: Cell Rep / Year: 2023
Title: Biochemical and biophysical characterization of natural polyreactivity in antibodies.
Authors: Borowska, M.T. / Boughter, C.T. / Bunker, J.J. / Guthmiller, J.J. / Wilson, P.C. / Roux, B. / Bendelac, A. / Adams, E.J.
History
DepositionJan 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 43G10 Fab heavy chain
B: 43G10 Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,4802
Polymers49,4802
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-26 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.240, 108.470, 115.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Antibody 43G10 Fab heavy chain


Mass: 24195.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody 43G10 Fab light chain


Mass: 25285.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.95 Å3/Da / Density % sol: 68.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16% PEG 4000, 0.2M Ammonium sulfate, 0.1M HEPES pH 7.5, 10% Isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.63→79.15 Å / Num. obs: 97569 / % possible obs: 99.33 % / Redundancy: 23 % / Biso Wilson estimate: 26.58 Å2 / CC1/2: 0.741 / Net I/σ(I): 18.9
Reflection shellResolution: 1.634→1.692 Å / Num. unique obs: 9583 / CC1/2: 0.0942

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→79.15 Å / SU ML: 0.2706 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.8347
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2455 4874 5.03 %
Rwork0.2242 92104 -
obs0.2253 96978 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.49 Å2
Refinement stepCycle: LAST / Resolution: 1.63→79.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 0 299 3735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653554
X-RAY DIFFRACTIONf_angle_d0.8744838
X-RAY DIFFRACTIONf_chiral_restr0.0561545
X-RAY DIFFRACTIONf_plane_restr0.0071616
X-RAY DIFFRACTIONf_dihedral_angle_d14.44251282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.650.52111150.44122801X-RAY DIFFRACTION91.01
1.65-1.670.43381570.42462927X-RAY DIFFRACTION96.07
1.67-1.690.391730.40152989X-RAY DIFFRACTION98.26
1.69-1.710.43231680.38943007X-RAY DIFFRACTION99.13
1.71-1.740.3861620.37143067X-RAY DIFFRACTION99.66
1.74-1.760.34451550.35583034X-RAY DIFFRACTION99.84
1.76-1.790.37261590.33893074X-RAY DIFFRACTION99.85
1.79-1.810.35111510.3243066X-RAY DIFFRACTION99.88
1.81-1.840.30981580.31193053X-RAY DIFFRACTION99.84
1.84-1.870.33281360.31373099X-RAY DIFFRACTION99.85
1.87-1.90.31161580.29973032X-RAY DIFFRACTION99.72
1.9-1.940.33351550.28213094X-RAY DIFFRACTION99.72
1.94-1.970.29431530.26133037X-RAY DIFFRACTION99.84
1.97-2.010.25931740.24223086X-RAY DIFFRACTION99.79
2.01-2.060.28111750.24183046X-RAY DIFFRACTION99.97
2.06-2.110.26731790.2313019X-RAY DIFFRACTION99.88
2.11-2.160.27321680.23073096X-RAY DIFFRACTION99.91
2.16-2.220.28561610.22713074X-RAY DIFFRACTION99.91
2.22-2.280.26441750.23083041X-RAY DIFFRACTION99.81
2.28-2.360.23311650.22793087X-RAY DIFFRACTION99.85
2.36-2.440.28121720.23313083X-RAY DIFFRACTION99.94
2.44-2.540.26871560.2233096X-RAY DIFFRACTION99.97
2.54-2.650.23271640.23083102X-RAY DIFFRACTION99.82
2.65-2.790.27641740.22333087X-RAY DIFFRACTION99.69
2.79-2.970.23571340.23063142X-RAY DIFFRACTION99.79
2.97-3.20.23451560.22593127X-RAY DIFFRACTION99.91
3.2-3.520.24731860.20573105X-RAY DIFFRACTION100
3.52-4.030.21781840.18783136X-RAY DIFFRACTION99.79
4.03-5.080.17661650.15783171X-RAY DIFFRACTION99.7
5.08-79.150.18711860.20143326X-RAY DIFFRACTION99.52

+
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