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- PDB-7kqy: Crystal Structure and Characterization of Human Heavy-Chain only ... -

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Basic information

Entry
Database: PDB / ID: 7kqy
TitleCrystal Structure and Characterization of Human Heavy-Chain only Antibodies reveals a novel, stable dimeric structure similar to Monoclonal Antibodies
ComponentsHeavy-Chain only Human Antibodies
KeywordsIMMUNE SYSTEM / antibody / human heavy-chain dimer
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.913 Å
AuthorsBahmanjah, S. / Mieczkowski, C. / Yu, Y. / Baker, J. / Raghunathan, G. / Tomazela, D. / Hsieh, M. / Mccoy, M. / Strickland, C. / Fayadat-Dilman, L.
CitationJournal: Antibodies / Year: 2020
Title: Crystal Structure and Characterization of Human Heavy-Chain Only Antibodies Reveals a Novel, Stable Dimeric Structure Similar to Monoclonal Antibodies.
Authors: Mieczkowski, C. / Bahmanjah, S. / Yu, Y. / Baker, J. / Raghunathan, G. / Tomazela, D. / Hsieh, M. / McCoy, M. / Strickland, C. / Fayadat-Dilman, L.
History
DepositionNov 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Nov 20, 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
A: Heavy-Chain only Human Antibodies
B: Heavy-Chain only Human Antibodies
C: Heavy-Chain only Human Antibodies
D: Heavy-Chain only Human Antibodies
E: Heavy-Chain only Human Antibodies
F: Heavy-Chain only Human Antibodies


Theoretical massNumber of molelcules
Total (without water)284,4656
Polymers284,4656
Non-polymers00
Water00
1
A: Heavy-Chain only Human Antibodies
B: Heavy-Chain only Human Antibodies


Theoretical massNumber of molelcules
Total (without water)94,8222
Polymers94,8222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-27 kcal/mol
Surface area18590 Å2
MethodPISA
2
C: Heavy-Chain only Human Antibodies
D: Heavy-Chain only Human Antibodies


Theoretical massNumber of molelcules
Total (without water)94,8222
Polymers94,8222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-29 kcal/mol
Surface area18840 Å2
MethodPISA
3
E: Heavy-Chain only Human Antibodies
F: Heavy-Chain only Human Antibodies


Theoretical massNumber of molelcules
Total (without water)94,8222
Polymers94,8222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-27 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.619, 73.418, 140.408
Angle α, β, γ (deg.)90.00, 125.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
Heavy-Chain only Human Antibodies


Mass: 47410.781 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae gen. sp. (mammal)
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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion
Details: 0.2 M Ammonium Sulfate, 0.1M Bis-Tris pH 5.5, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.91→114.1 Å / Num. obs: 22757 / % possible obs: 75 % / Redundancy: 2 % / CC1/2: 0.979 / Net I/σ(I): 4.85
Reflection shellResolution: 2.91→3.02 Å / Num. unique obs: 131 / CC1/2: 0.619

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.27data extraction
PHENIX1.14_3260model building
XDSdata scaling
PHASER1.14_3260phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vsi

5vsi


Resolution: 2.913→114.009 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.13 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.26 1082 4.76 %
Rwork0.2072 --
obs0.2097 22742 73.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.913→114.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9265 0 0 0 9265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149512
X-RAY DIFFRACTIONf_angle_d1.8512983
X-RAY DIFFRACTIONf_dihedral_angle_d11.6196191
X-RAY DIFFRACTIONf_chiral_restr0.1581508
X-RAY DIFFRACTIONf_plane_restr0.0131618

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