[English] 日本語
Yorodumi
- PDB-8bl6: De novo single-chain immunoglobulin dimer scIg12+EF3a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bl6
TitleDe novo single-chain immunoglobulin dimer scIg12+EF3a
ComponentsdIG14-scdim-EF62
KeywordsDE NOVO PROTEIN / de novo / immunoglobulin / single-chain dimer / sandwich / beta / EF-hand
Function / homologyTERBIUM(III) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNadal, M. / Roel-Touris, J. / Marcos, E.
Funding supportEuropean Union, Spain, 2items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 145-2021European Union
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Nat Commun / Year: 2023
Title: Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops.
Authors: Roel-Touris, J. / Nadal, M. / Marcos, E.
History
DepositionNov 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dIG14-scdim-EF62
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7105
Polymers20,1411
Non-polymers5694
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-23 kcal/mol
Surface area7370 Å2
Unit cell
Length a, b, c (Å)73.841, 73.841, 96.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein dIG14-scdim-EF62


Mass: 20141.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tb
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG MME 2000 20.0%w/v, TRIS 0.1M pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.50102 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2022
RadiationMonochromator: 1.50102 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.50102 Å / Relative weight: 1
ReflectionResolution: 2.8→58.59 Å / Num. obs: 7030 / % possible obs: 100 % / Redundancy: 16.2 % / CC1/2: 0.944 / Rmerge(I) obs: 0.016 / Net I/σ(I): 15.4
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 1001 / CC1/2: 0.876

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model prediction

Resolution: 2.8→58.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.006 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25711 724 10.4 %RANDOM
Rwork0.20182 ---
obs0.20744 6261 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.072 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å20 Å2
2--0.6 Å20 Å2
3----1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.8→58.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 9 0 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171081
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.6671566
X-RAY DIFFRACTIONr_angle_other_deg1.1221.592505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8365137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56321.02678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.36615208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1511514
X-RAY DIFFRACTIONr_chiral_restr0.0630.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.389.239554
X-RAY DIFFRACTIONr_mcbond_other8.279.22552
X-RAY DIFFRACTIONr_mcangle_it12.05513.853689
X-RAY DIFFRACTIONr_mcangle_other11.96913.858689
X-RAY DIFFRACTIONr_scbond_it10.71910.713605
X-RAY DIFFRACTIONr_scbond_other10.71510.718606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.81415.537875
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 55 -
Rwork0.381 441 -
obs--99.6 %

+
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