[English] 日本語
Yorodumi
- PDB-6rbb: CRYSTAL STRUCTURE OF the VhH-domain of anti-IL-17A antibody netakimab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rbb
TitleCRYSTAL STRUCTURE OF the VhH-domain of anti-IL-17A antibody netakimab
ComponentsVHH domain of netakimab
KeywordsIMMUNE SYSTEM / VHH / antibody netakimab / complementarity determining regions / IL-17A / psoriasis
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKostareva, O.S. / Kolyadenko, I.A. / Ulitin, A.B. / Ekimova, V.M. / Evdokimov, S.R. / Garber, M.B. / Tishchenko, T.V. / Gabdulkhakov, A.G.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation17-74-10156 Russian Federation
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF the VhH-domain of anti-IL-17A antibody netakimab
Authors: Kostareva, O.S. / Kolyadenko, I.A. / Ulitin, A.B. / Ekimova, V.M. / Evdokimov, S.R. / Garber, M.B. / Tishchenko, T.V. / Gabdulkhakov, A.G.
History
DepositionApr 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: VHH domain of netakimab
I: VHH domain of netakimab
J: VHH domain of netakimab
K: VHH domain of netakimab


Theoretical massNumber of molelcules
Total (without water)52,9674
Polymers52,9674
Non-polymers00
Water46826
1
H: VHH domain of netakimab


Theoretical massNumber of molelcules
Total (without water)13,2421
Polymers13,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: VHH domain of netakimab


Theoretical massNumber of molelcules
Total (without water)13,2421
Polymers13,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
J: VHH domain of netakimab


Theoretical massNumber of molelcules
Total (without water)13,2421
Polymers13,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: VHH domain of netakimab


Theoretical massNumber of molelcules
Total (without water)13,2421
Polymers13,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.872, 72.499, 129.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Antibody
VHH domain of netakimab


Mass: 13241.626 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Cricetulus griseus (Chinese hamster)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50mMNa AcpH 5.5, 150mMNaCl with 0.1M Citrate pH 5, 20% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 21024 / % possible obs: 98.3 % / Redundancy: 5.1 % / CC1/2: 0.996 / Rrim(I) all: 0.154 / Net I/σ(I): 9.1
Reflection shellResolution: 2.38→2.52 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3076 / % possible all: 90.7

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QKD

6qkd


Resolution: 2.45→41.846 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 32.24
RfactorNum. reflection% reflection
Rfree0.2801 1889 5.18 %
Rwork0.2155 --
obs0.2188 19563 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→41.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3661 0 0 26 3687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093762
X-RAY DIFFRACTIONf_angle_d1.0535097
X-RAY DIFFRACTIONf_dihedral_angle_d17.7592358
X-RAY DIFFRACTIONf_chiral_restr0.053535
X-RAY DIFFRACTIONf_plane_restr0.005667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.51630.38071500.33752702X-RAY DIFFRACTION100
2.5163-2.59030.3771740.31962643X-RAY DIFFRACTION100
2.5903-2.67390.33821610.30332627X-RAY DIFFRACTION100
2.6739-2.76940.31581470.29252657X-RAY DIFFRACTION99
2.7694-2.88030.3731140.27472689X-RAY DIFFRACTION99
2.8803-3.01130.36851310.25442671X-RAY DIFFRACTION100
3.0113-3.17010.37511540.24892629X-RAY DIFFRACTION99
3.1701-3.36860.33461370.23642691X-RAY DIFFRACTION99
3.3686-3.62850.25981570.1982648X-RAY DIFFRACTION99
3.6285-3.99340.22671390.1852665X-RAY DIFFRACTION100
3.9934-4.57070.18531680.152666X-RAY DIFFRACTION100
4.5707-5.75620.23471280.17022648X-RAY DIFFRACTION99
5.7562-41.85240.26851290.17982665X-RAY DIFFRACTION99

+
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