[English] 日本語
Yorodumi
- PDB-6kx0: Crystal structure of SN-101 mAb non-liganded form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kx0
TitleCrystal structure of SN-101 mAb non-liganded form
Components
  • Fab Fragment-SN-101-Heavy chain
  • Fab Fragment-SN-101-Light chain
KeywordsIMMUNE SYSTEM / Antibody / IgG1 / MUC1 / Glycopeptide
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsWakui, H. / Tanaka, Y. / Kato, K. / Ose, T. / Matsumoto, I. / Min, Y. / Tachibana, T. / Nishimura, S.-I.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25220206 Japan
Japan Society for the Promotion of Science19H00918 Japan
CitationJournal: Chem Sci / Year: 2020
Title: A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes
Authors: Wakui, H. / Tanaka, Y. / Ose, T. / Matsumoto, I. / Kato, K. / Min, Y. / Tachibana, T. / Sato, M. / Naruchi, K. / Martin, F.G. / Hinou, H. / Nishimura, S.-I.
History
DepositionSep 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fab Fragment-SN-101-Heavy chain
B: Fab Fragment-SN-101-Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2254
Polymers51,9802
Non-polymers2442
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-18 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.860, 40.100, 67.780
Angle α, β, γ (deg.)90.000, 99.830, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Antibody Fab Fragment-SN-101-Heavy chain


Mass: 25541.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab Fragment-SN-101-Light chain


Mass: 26438.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 300-350 mM NaSCN 20-30% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16818 / % possible obs: 99.6 % / Redundancy: 4.99 % / Rrim(I) all: 0.101 / Net I/σ(I): 12.78
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 5.08 % / Num. unique obs: 2665 / Rrim(I) all: 0.663 / % possible all: 98.9

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ5

1pz5


Resolution: 2.404→39.378 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2779 842 5.01 %
Rwork0.2254 --
obs0.2278 16816 99.68 %
Displacement parametersBiso mean: 51.59 Å2
Refinement stepCycle: LAST / Resolution: 2.404→39.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 16 37 3348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033392
X-RAY DIFFRACTIONf_angle_d0.6264618
X-RAY DIFFRACTIONf_chiral_restr0.0413515
X-RAY DIFFRACTIONf_plane_restr0.0042586
X-RAY DIFFRACTIONf_dihedral_angle_d11.24282017

+
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