[English] 日本語
Yorodumi
- PDB-6dla: Crystal structures of an influenza A hemagglutinin antibody Fab C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dla
TitleCrystal structures of an influenza A hemagglutinin antibody Fab CH65:7969d2
Components
  • CH65:7969d2 Fab heavy chain
  • CH65:7969d2 Fab light chain
KeywordsIMMUNE SYSTEM / Influenza A virus / hemagglutinin / antibody / antibody design / rosetta
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsDong, J. / Crowe, J.E. / Finn, J.A.
CitationJournal: Structure / Year: 2020
Title: Identification of Structurally Related Antibodies in Antibody Sequence Databases Using Rosetta-Derived Position-Specific Scoring.
Authors: Finn, J.A. / Dong, J. / Sevy, A.M. / Parrish, E. / Gilchuk, I. / Nargi, R. / Scarlett-Jones, M. / Reichard, W. / Bombardi, R. / Voss, T.G. / Meiler, J. / Crowe Jr., J.E.
History
DepositionMay 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 11, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: CH65:7969d2 Fab heavy chain
L: CH65:7969d2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4353
Polymers47,3392
Non-polymers961
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-30 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.378, 67.238, 130.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody CH65:7969d2 Fab heavy chain


Mass: 24577.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody CH65:7969d2 Fab light chain


Mass: 22761.139 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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 291.16 K / Method: evaporation / Details: AmSO4 1.8-2.2M, Bis-Tris 100 mM pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 2→46.8 Å / Num. obs: 34481 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.391 / Num. unique all: 4897

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wuk

4wuk


Resolution: 2.004→43.646 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 1697 4.95 %
Rwork0.1777 --
obs0.1791 34265 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.004→43.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 5 308 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073355
X-RAY DIFFRACTIONf_angle_d0.8364595
X-RAY DIFFRACTIONf_dihedral_angle_d6.5681965
X-RAY DIFFRACTIONf_chiral_restr0.058519
X-RAY DIFFRACTIONf_plane_restr0.006589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0045-2.06350.30281350.21842468X-RAY DIFFRACTION92
2.0635-2.13010.23911370.20112689X-RAY DIFFRACTION99
2.1301-2.20620.27041360.20222685X-RAY DIFFRACTION99
2.2062-2.29450.24241350.19692686X-RAY DIFFRACTION99
2.2945-2.3990.2511380.20082704X-RAY DIFFRACTION99
2.399-2.52540.2381400.19972688X-RAY DIFFRACTION100
2.5254-2.68360.22431460.19352712X-RAY DIFFRACTION100
2.6836-2.89080.21511440.19452717X-RAY DIFFRACTION100
2.8908-3.18160.20831450.18362757X-RAY DIFFRACTION100
3.1816-3.64180.18431580.16462727X-RAY DIFFRACTION100
3.6418-4.58750.16281390.14712801X-RAY DIFFRACTION100
4.5875-43.65650.19331440.16992934X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.9865 Å / Origin y: -9.3592 Å / Origin z: -51.37 Å
111213212223313233
T0.2058 Å20.0226 Å2-0.0213 Å2-0.2237 Å2-0.003 Å2--0.2402 Å2
L0.4968 °20.0874 °2-0.557 °2-0.493 °20.0319 °2--1.0668 °2
S0.0448 Å °0.0136 Å °0.0974 Å °0.106 Å °0.0033 Å °-0.0273 Å °-0.1076 Å °-0.0087 Å °-0.0545 Å °
Refinement TLS groupSelection details: all

+
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