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- PDB-6dl8: Crystal Structure of an influenza A hemagglutinin antibody Fab va... -

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Basic information

Entry
Database: PDB / ID: 6dl8
TitleCrystal Structure of an influenza A hemagglutinin antibody Fab variant CH67:1203d4 chimera
Components
  • CH67:1203d4 FAB light chain
  • Ch67:1203d4 FAB heavy chain
KeywordsIMMUNE SYSTEM / influenza A / 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: 3.805 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: CH67:1203d4 FAB light chain
H: Ch67:1203d4 FAB heavy chain
B: CH67:1203d4 FAB light chain
A: Ch67:1203d4 FAB heavy chain


Theoretical massNumber of molelcules
Total (without water)94,7334
Polymers94,7334
Non-polymers00
Water00
1
L: CH67:1203d4 FAB light chain
H: Ch67:1203d4 FAB heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3672
Polymers47,3672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-22 kcal/mol
Surface area20510 Å2
MethodPISA
2
B: CH67:1203d4 FAB light chain
A: Ch67:1203d4 FAB heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3672
Polymers47,3672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-23 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.235, 73.695, 76.848
Angle α, β, γ (deg.)62.91, 88.86, 62.07
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody CH67:1203d4 FAB light chain


Mass: 22671.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Ch67:1203d4 FAB heavy chain


Mass: 24694.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

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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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 291.16 K / Method: evaporation / Details: 15% v/v IPA, 0.1M NaCit pH 5.0, 10% PEG 10000

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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: 3.8→40.53 Å / Num. obs: 11641 / % possible obs: 98.1 % / Redundancy: 1.8 % / Rsym value: 0.059 / Net I/σ(I): 10.1
Reflection shellResolution: 3.8→4.01 Å / Rmerge(I) obs: 0.113 / Num. unique all: 1661

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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: 4HKX

4hkx


Resolution: 3.805→30.93 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 528 4.56 %
Rwork0.2329 --
obs0.2352 11576 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.805→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5583 0 0 0 5583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025735
X-RAY DIFFRACTIONf_angle_d0.5817888
X-RAY DIFFRACTIONf_dihedral_angle_d2.3273299
X-RAY DIFFRACTIONf_chiral_restr0.046862
X-RAY DIFFRACTIONf_plane_restr0.0051064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8047-4.18670.28111580.24012669X-RAY DIFFRACTION96
4.1867-4.79060.2882840.20852839X-RAY DIFFRACTION99
4.7906-6.02840.28271290.2342801X-RAY DIFFRACTION99
6.0284-30.93110.28391570.24742739X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 15.2648 Å / Origin y: -22.9376 Å / Origin z: 20.2336 Å
111213212223313233
T0.4323 Å2-0.0506 Å20.1009 Å2-0.3181 Å20.0395 Å2--0.409 Å2
L0.5746 °2-0.0028 °20.0346 °2-0.1145 °2-0.2182 °2--1.276 °2
S0.004 Å °-0.028 Å °0.0058 Å °-0.0348 Å °-0.0194 Å °-0.052 Å °0.0695 Å °-0.0517 Å °0.0094 Å °
Refinement TLS groupSelection details: all

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