[English] 日本語
Yorodumi
- PDB-6tkc: ChiLob 7/4 H2 HC-C225S F(ab')2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tkc
TitleChiLob 7/4 H2 HC-C225S F(ab')2
Components
  • Chilob 7/4 H2 heavy chain C225S
  • Chilob 7/4 H2 kappa chain
KeywordsIMMUNE SYSTEM / ----
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsOrr, C.M. / Fisher, H. / Tews, I.
CitationJournal: Sci Immunol / Year: 2022
Title: Hinge disulfides in human IgG2 CD40 antibodies modulate receptor signaling by regulation of conformation and flexibility.
Authors: Orr, C.M. / Fisher, H. / Yu, X. / Chan, C.H. / Gao, Y. / Duriez, P.J. / Booth, S.G. / Elliott, I. / Inzhelevskaya, T. / Mockridge, I. / Penfold, C.A. / Wagner, A. / Glennie, M.J. / White, A. ...Authors: Orr, C.M. / Fisher, H. / Yu, X. / Chan, C.H. / Gao, Y. / Duriez, P.J. / Booth, S.G. / Elliott, I. / Inzhelevskaya, T. / Mockridge, I. / Penfold, C.A. / Wagner, A. / Glennie, M.J. / White, A.L. / Essex, J.W. / Pearson, A.R. / Cragg, M.S. / Tews, I.
History
DepositionNov 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Derived calculations
Category: atom_type / citation ...atom_type / citation / citation_author / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
HHH: Chilob 7/4 H2 heavy chain C225S
LLL: Chilob 7/4 H2 kappa chain


Theoretical massNumber of molelcules
Total (without water)48,5632
Polymers48,5632
Non-polymers00
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-29 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.421, 149.421, 45.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

#1: Antibody Chilob 7/4 H2 heavy chain C225S


Mass: 25099.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Chilob 7/4 H2 kappa chain


Mass: 23463.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4000, HEPES

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.755 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jan 24, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.755 Å / Relative weight: 1
ReflectionResolution: 2.3→129.4 Å / Num. obs: 24537 / % possible obs: 93.6 % / Redundancy: 40.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.023 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 34.2 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2058 / CC1/2: 0.85 / Rpim(I) all: 0.154 / % possible all: 85

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→74.823 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.194 / Average fsc free: 0.9083 / Average fsc work: 0.9264 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.218
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2359 1193 4.862 %
Rwork0.1834 23343 -
all0.186 --
obs-24536 93.307 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.852 Å2
Baniso -1Baniso -2Baniso -3
1--0.279 Å2-0.14 Å20 Å2
2---0.279 Å20 Å2
3---0.906 Å2
Refinement stepCycle: LAST / Resolution: 2.3→74.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 0 239 3482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133334
X-RAY DIFFRACTIONr_bond_other_d0.0370.0172928
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.6474544
X-RAY DIFFRACTIONr_angle_other_deg2.471.576850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7145425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78924.058138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52215530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.074158
X-RAY DIFFRACTIONr_chiral_restr0.0660.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023725
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02655
X-RAY DIFFRACTIONr_nbd_refined0.2030.2522
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.22715
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21521
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21436
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2205
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2430.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0980.25
X-RAY DIFFRACTIONr_nbd_other0.1940.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.28
X-RAY DIFFRACTIONr_mcbond_it4.1574.6331709
X-RAY DIFFRACTIONr_mcbond_other4.1534.6311708
X-RAY DIFFRACTIONr_mcangle_it6.0216.9242131
X-RAY DIFFRACTIONr_mcangle_other6.026.9282132
X-RAY DIFFRACTIONr_scbond_it4.65.1211625
X-RAY DIFFRACTIONr_scbond_other4.5975.1191624
X-RAY DIFFRACTIONr_scangle_it6.8477.4692413
X-RAY DIFFRACTIONr_scangle_other6.8437.472413
X-RAY DIFFRACTIONr_lrange_it9.18953.6893507
X-RAY DIFFRACTIONr_lrange_other9.13453.4583454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.286900.2381515X-RAY DIFFRACTION84.6073
2.36-2.4240.256620.2411535X-RAY DIFFRACTION84.7665
2.424-2.4950.266810.2161533X-RAY DIFFRACTION88.5354
2.495-2.5710.242830.2171497X-RAY DIFFRACTION88.764
2.571-2.6560.301700.2171466X-RAY DIFFRACTION88.5813
2.656-2.7490.37510.2231459X-RAY DIFFRACTION90.9091
2.749-2.8530.25870.2141402X-RAY DIFFRACTION92.3697
2.853-2.9690.259760.1981341X-RAY DIFFRACTION92.6749
2.969-3.1010.274750.1941337X-RAY DIFFRACTION94.8925
3.101-3.2520.216620.1951323X-RAY DIFFRACTION94.928
3.252-3.4280.272700.1951244X-RAY DIFFRACTION98.7228
3.428-3.6360.253560.1951230X-RAY DIFFRACTION98.6196
3.636-3.8870.211650.1731137X-RAY DIFFRACTION100
3.887-4.1980.205630.1751071X-RAY DIFFRACTION100
4.198-4.5980.218520.1411006X-RAY DIFFRACTION100
4.598-5.140.236390.136907X-RAY DIFFRACTION100
5.14-5.9330.176450.147785X-RAY DIFFRACTION100
5.933-7.2630.251490.188667X-RAY DIFFRACTION100

+
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