[English] 日本語
Yorodumi
- PDB-6qn9: Structure of bovine anti-RSV Fab B4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qn9
TitleStructure of bovine anti-RSV Fab B4
Components
  • Heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / cattle antibodies / bovine respiratory syncytial virus / anti-RSV B4 / anti-RSV B13 / hybrid Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsRen, J. / Nettleship, J.E. / Harris, G. / Mwangi, W. / Rhaman, N. / Grant, C. / Kotecha, A. / Fry, E. / Charleston, B. / Stuart, D.I. ...Ren, J. / Nettleship, J.E. / Harris, G. / Mwangi, W. / Rhaman, N. / Grant, C. / Kotecha, A. / Fry, E. / Charleston, B. / Stuart, D.I. / Hammond, J. / Owens, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101122/Z/13/Z United Kingdom
CitationJournal: Mol.Immunol. / Year: 2019
Title: The role of the light chain in the structure and binding activity of two cattle antibodies that neutralize bovine respiratory syncytial virus.
Authors: Ren, J. / Nettleship, J.E. / Harris, G. / Mwangi, W. / Rhaman, N. / Grant, C. / Kotecha, A. / Fry, E. / Charleston, B. / Stuart, D.I. / Hammond, J. / Owens, R.J.
History
DepositionFeb 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0905
Polymers47,8102
Non-polymers2803
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-47 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.335, 134.873, 42.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Antibody Heavy chain


Mass: 25134.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Homo sapiens (human)
#2: Antibody light chain


Mass: 22676.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium Sulphate 25.0% w/v Polyethylene Glycol 3350 0.1 M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.89→67.7 Å / Num. obs: 36744 / % possible obs: 100 % / Redundancy: 23.6 % / CC1/2: 1 / Rmerge(I) obs: 0.129 / Net I/σ(I): 11.5
Reflection shellResolution: 1.89→1.92 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1790 / CC1/2: 0.967 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX(dev_3386: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DGG

3dgg


Resolution: 1.89→67.7 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.19
RfactorNum. reflection% reflection
Rfree0.2541 1819 4.98 %
Rwork0.2281 --
obs0.2294 36494 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→67.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 0 17 72 3072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033058
X-RAY DIFFRACTIONf_angle_d0.6624161
X-RAY DIFFRACTIONf_dihedral_angle_d13.2731835
X-RAY DIFFRACTIONf_chiral_restr0.047484
X-RAY DIFFRACTIONf_plane_restr0.005523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8888-1.93990.34451390.36272601X-RAY DIFFRACTION99
1.9399-1.99690.36361520.3082608X-RAY DIFFRACTION99
1.9969-2.06140.30691090.29422634X-RAY DIFFRACTION99
2.0614-2.13510.31041390.26542637X-RAY DIFFRACTION99
2.1351-2.22060.28141420.25052631X-RAY DIFFRACTION99
2.2206-2.32160.30881180.24392623X-RAY DIFFRACTION99
2.3216-2.4440.27291360.23362642X-RAY DIFFRACTION99
2.444-2.59720.241520.23122627X-RAY DIFFRACTION99
2.5972-2.79770.28541530.23052671X-RAY DIFFRACTION100
2.7977-3.07930.26851560.22142650X-RAY DIFFRACTION100
3.0793-3.52480.26081420.22522713X-RAY DIFFRACTION100
3.5248-4.44080.23781320.20542748X-RAY DIFFRACTION100
4.4408-67.78220.20921490.21222890X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4844-0.18531.8340.8182-0.42185.5174-0.0095-0.01390.1687-0.0729-0.04490.01520.02950.27670.05830.4488-0.0243-0.00160.4725-0.02080.3887-8.915935.4323-23.9978
27.31455.0341-0.41543.8193-0.53640.2079-0.23270.0313-1.19010.03720.5751-1.453-0.4549-0.03620.11071.6977-0.30480.01320.6422-0.01291.4326-17.1264-4.5432-9.6981
31.97381.7175-0.12741.5103-0.12250.0294-0.83750.5567-0.0764-0.55680.2127-0.41640.283-0.2619-1.05151.6305-0.6262-0.0520.6671-0.0440.659-14.519912.9564-10.5903
43.58632.3724-0.74581.8626-0.48110.1539-0.53420.1995-0.7687-0.47350.1839-0.33580.19310.20790.10541.7721-0.37010.60750.96550.1941.2415-5.873110.2791-16.0718
55.94960.99870.30971.1462-0.42793.1830.05450.17520.0169-0.0394-0.1577-0.09280.0475-0.6480.01850.39940.0228-0.02090.4699-0.0220.3686-28.785732.8584-32.0391
60.42290.63260.47741.84920.43761.27640.2376-0.221-0.54020.3742-0.2191-0.07170.6359-0.0032-0.38931.5194-0.41540.04150.75260.08061.1278-25.33692.9411-12.176
72.7436-0.34111.33294.42481.28531.38580.3252-0.5913-0.1436-0.46060.08140.07150.4679-0.83760.23231.4801-0.5391-0.08520.82840.12180.8718-26.75835.1277-5.3097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 135 )
2X-RAY DIFFRACTION2chain 'H' and (resid 136 through 154 )
3X-RAY DIFFRACTION3chain 'H' and (resid 155 through 196 )
4X-RAY DIFFRACTION4chain 'H' and (resid 197 through 223 )
5X-RAY DIFFRACTION5chain 'L' and (resid 3 through 107 )
6X-RAY DIFFRACTION6chain 'L' and (resid 108 through 127 )
7X-RAY DIFFRACTION7chain 'L' and (resid 128 through 212 )

+
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