[English] 日本語
Yorodumi
- PDB-3qhf: Crystal Structure of Fab del2D1, a deletion variant of anti-influ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qhf
TitleCrystal Structure of Fab del2D1, a deletion variant of anti-influenza antibody 2D1
Components
  • Human monoclonal antibody del2D1, Fab Heavy Chain
  • Human monoclonal antibody del2D1, Fab Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Immune recognition / Influenza A virus hemagglutinin / Extracellular (secreted)
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.655 Å
AuthorsEkiert, D.C. / Wilson, I.A.
CitationJournal: MBio / Year: 2011
Title: An insertion mutation that distorts antibody binding site architecture enhances function of a human antibody.
Authors: Krause, J.C. / Ekiert, D.C. / Tumpey, T.M. / Smith, P.B. / Wilson, I.A. / Crowe, J.E.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 13, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Human monoclonal antibody del2D1, Fab Heavy Chain
L: Human monoclonal antibody del2D1, Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,0992
Polymers47,0992
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-26 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.913, 69.680, 97.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Human monoclonal antibody del2D1, Fab Heavy Chain


Mass: 24304.389 Da / Num. of mol.: 1 / Fragment: Fab Heavy Chain / Mutation: deletion of somatic insertion (ITY)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin gamma / Plasmid: pEE6.4 / Cell line (production host): 293F / Production host: Homo sapiens (human)
#2: Antibody Human monoclonal antibody del2D1, Fab Light Chain


Mass: 22795.078 Da / Num. of mol.: 1 / Fragment: Fab Light Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin lambda / Plasmid: pEE12.4 / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 4000, 100 mM sodium acetate, and 200 mM magnesium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 273K

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: Double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 55866 / Num. obs: 55730 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.65→1.71 Å / % possible all: 99.6

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QHZ (chains H and L)

3qhz


Resolution: 1.655→50 Å / SU ML: 0.21 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 2830 5.08 %Random
Rwork0.1831 ---
all0.1845 55866 --
obs0.1845 55730 98.1 %-
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.462 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.8687 Å20 Å2-0 Å2
2--4.8174 Å2-0 Å2
3---0.0513 Å2
Refinement stepCycle: LAST / Resolution: 1.655→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 0 273 3563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093475
X-RAY DIFFRACTIONf_angle_d1.2274766
X-RAY DIFFRACTIONf_dihedral_angle_d12.261241
X-RAY DIFFRACTIONf_chiral_restr0.078554
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.655-1.6830.3028860.2491867X-RAY DIFFRACTION69
1.683-1.71360.24071430.2332625X-RAY DIFFRACTION100
1.7136-1.74660.29091430.22922650X-RAY DIFFRACTION99
1.7466-1.78220.2291490.21032637X-RAY DIFFRACTION99
1.7822-1.8210.23561440.20742651X-RAY DIFFRACTION99
1.821-1.86340.21251470.20212619X-RAY DIFFRACTION99
1.8634-1.910.25391530.20132633X-RAY DIFFRACTION99
1.91-1.96160.27571290.1932698X-RAY DIFFRACTION99
1.9616-2.01930.20811370.1962627X-RAY DIFFRACTION99
2.0193-2.08450.22111600.18012655X-RAY DIFFRACTION99
2.0845-2.1590.21271380.18482675X-RAY DIFFRACTION99
2.159-2.24540.20821270.18252690X-RAY DIFFRACTION100
2.2454-2.34760.21721410.19132694X-RAY DIFFRACTION100
2.3476-2.47140.21871400.19142690X-RAY DIFFRACTION100
2.4714-2.62620.21941400.20862689X-RAY DIFFRACTION100
2.6262-2.8290.25831290.19742728X-RAY DIFFRACTION100
2.829-3.11360.19691240.1942736X-RAY DIFFRACTION100
3.1136-3.56390.21931800.18092700X-RAY DIFFRACTION100
3.5639-4.48950.19091400.15452787X-RAY DIFFRACTION100
4.4895-43.81180.1781800.17112849X-RAY DIFFRACTION99
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)
10.94320.150.24342.40940.51944.1313-0.0823-0.1094-0.10560.09110.0819-0.15570.12380.21010.00310.13080.05860.01880.25950.05180.1965-0.5435-25.52938.2463
22.87370.2425-0.10222.9552-1.56423.1685-0.06650.22580.2194-0.1415-0.0756-0.05960.01390.170.1450.1893-0.0094-0.0220.18160.01870.17523.5423-14.7771-22.2556
33.0626-0.2290.04682.9253-0.30972.77180.2312-0.21710.43540.0224-0.196-0.1336-0.41620.1988-0.04770.2331-0.00910.03560.2787-0.00390.255-2.6215-5.612113.5923
42.0963-0.74080.02884.4433-0.63973.75580.06390.0227-0.05880.25460.11950.1569-0.0612-0.1007-0.16120.19780.00180.00950.1630.01840.1867-7.5946-3.9509-24.6762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain H and resid 1:113
2X-RAY DIFFRACTION2chain H and resid 114:232
3X-RAY DIFFRACTION3chain L and resid 1:108
4X-RAY DIFFRACTION4chain L and resid 109:213

+
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