[English] 日本語
Yorodumi
- PDB-6gxx: Fab fragment of an antibody selective for alpha-1-antitrypsin in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gxx
TitleFab fragment of an antibody selective for alpha-1-antitrypsin in the native conformation
Components
  • FAB 1D9 heavy chain
  • FAB 1D9 light chain
KeywordsPROTEIN BINDING / Antibody fragment / Antitrypsin binding / Diagnostic / Monoclonal / conformationally-selective
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsElliston, E.L.K. / Miranda, E. / Perez, J. / Lomas, D.A. / Irving, J.A.
Funding support United Kingdom, United States, 5items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N024842/1 United Kingdom
Wellcome TrustWellcome Trust 4-year PhD Interdisciplinary Programme in Structural, Computational and Chemical Biology United Kingdom
Other privateAlpha-1 Foundation project grant to James Irving United States
Other privateAlpha-1 Foundation pilot grant to Elena Miranda United States
Other governmentUCLH/NIHR Biomedical Research Centre United Kingdom
CitationJournal: To Be Published
Title: Characterisation of a monoclonal antibody conformationally-selective for native alpha-1-antitrypsin
Authors: Elliston, E.L.K. / Miranda, E. / Perez, J. / Irving, J.A. / Lomas, D.A.
History
DepositionJun 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: FAB 1D9 heavy chain
L: FAB 1D9 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0453
Polymers48,0202
Non-polymers241
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-41 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.103, 85.257, 89.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11H-586-

HOH

21L-492-

HOH

31L-510-

HOH

41L-569-

HOH

51L-687-

HOH

-
Components

#1: Antibody FAB 1D9 heavy chain


Mass: 24161.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Organ: Spleen / Variant: BALB/c
#2: Antibody FAB 1D9 light chain


Mass: 23859.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Organ: Spleen / Variant: BALB/c
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.13 Å3/Da / Density % sol: 42.21 % / Description: Tabular
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3350, 0.1M Hepes, 0.05M magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2018
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.85→29.81 Å / Num. obs: 34148 / % possible obs: 94.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 19.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.039 / Rrim(I) all: 0.139 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.8911.7421160.9350.2270.78398.1
9.08-29.8110.531.93560.9990.020.06997.2

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XDS20171218data reduction
Aimlessv0.6.2data scaling
PHASERv2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mf2

1mf2


Resolution: 1.85→27.08 Å / SU ML: 0.2351 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4849
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 1718 5.05 %Random
Rwork0.186 ---
obs0.1878 34004 94.75 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 19.96 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 1 584 3831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373389
X-RAY DIFFRACTIONf_angle_d0.63734649
X-RAY DIFFRACTIONf_chiral_restr0.046531
X-RAY DIFFRACTIONf_plane_restr0.0044593
X-RAY DIFFRACTIONf_dihedral_angle_d11.8671203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.3751540.30062737X-RAY DIFFRACTION98.17
1.91-1.970.3027850.23871758X-RAY DIFFRACTION63.31
1.97-2.040.24031590.20062798X-RAY DIFFRACTION100
2.04-2.120.26981590.19572784X-RAY DIFFRACTION100
2.12-2.220.23291590.19672799X-RAY DIFFRACTION99.7
2.22-2.330.27831110.24532226X-RAY DIFFRACTION78.63
2.33-2.480.24661510.19552811X-RAY DIFFRACTION100
2.48-2.670.25111530.19142821X-RAY DIFFRACTION99.97
2.67-2.940.21971370.18482869X-RAY DIFFRACTION100
2.94-3.360.2061460.16782870X-RAY DIFFRACTION100
3.36-4.240.16691470.16062779X-RAY DIFFRACTION96.19
4.24-27.090.1971570.16673034X-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