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- PDB-6dlb: Crystal Structure of an influenza A hemagglutinin antibody Fab CH... -

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Basic information

Entry
Database: PDB / ID: 6dlb
TitleCrystal Structure of an influenza A hemagglutinin antibody Fab CH65:1203d4 chimera
Components
  • CH65:1203d4 Fab heavy chain
  • CH65:1203d4 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: 2.2 Å
AuthorsDong, J. / Finn, J.A. / Crowe, J.E.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: CH65:1203d4 Fab heavy chain
L: CH65:1203d4 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4653
Polymers47,3692
Non-polymers961
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-32 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.493, 67.297, 130.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody CH65:1203d4 Fab heavy chain


Mass: 24591.500 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 CH65:1203d4 Fab light chain


Mass: 22777.139 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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 291.16 K / Method: evaporation / Details: AmSO4 1.8-2.2M, Tris 100 mM pH 8.3

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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: 2.2→46.91 Å / Num. obs: 26563 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.614 / Num. unique all: 3819

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Processing

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

4wuk


Resolution: 2.2→43.186 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 1279 4.83 %
Rwork0.1903 --
obs0.1918 26495 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→43.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 5 208 3479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063360
X-RAY DIFFRACTIONf_angle_d0.5994600
X-RAY DIFFRACTIONf_dihedral_angle_d4.9861970
X-RAY DIFFRACTIONf_chiral_restr0.046518
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28810.31541270.25322778X-RAY DIFFRACTION100
2.2881-2.39220.29221310.23242773X-RAY DIFFRACTION100
2.3922-2.51830.27631430.23012740X-RAY DIFFRACTION100
2.5183-2.67610.25871700.2272745X-RAY DIFFRACTION100
2.6761-2.88270.29841270.2252782X-RAY DIFFRACTION100
2.8827-3.17270.25471380.20952796X-RAY DIFFRACTION100
3.1727-3.63160.22051680.18562767X-RAY DIFFRACTION100
3.6316-4.57460.17621470.15522838X-RAY DIFFRACTION100
4.5746-43.19460.17841280.16942997X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.9704 Å / Origin y: -9.2084 Å / Origin z: -51.3619 Å
111213212223313233
T0.2397 Å20.0217 Å2-0.0283 Å2-0.2782 Å20.0033 Å2--0.3123 Å2
L0.5185 °20.0655 °2-0.6151 °2-0.5631 °20.0845 °2--1.1391 °2
S0.0359 Å °0.0286 Å °0.0779 Å °0.0887 Å °-0.0028 Å °-0.0238 Å °-0.0763 Å °-0.004 Å °-0.0427 Å °
Refinement TLS groupSelection details: all

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