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- PDB-2hwz: Fab fragment of Humanized anti-viral antibody MEDI-493 (Synagis TM) -

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Basic information

Entry
Database: PDB / ID: 2hwz
TitleFab fragment of Humanized anti-viral antibody MEDI-493 (Synagis TM)
Components
  • Immunoglobulin Fab heavy chain
  • Immunoglobulin Fab light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBraden, B.
Citation
Journal: To be Published
Title: Identification of a single tryptophan residue as critical for binding activity in a humanized monoclonal antibody against respiratory syncytial virus
Authors: Wei, Z. / Feng, J. / Lin, H.-Y. / Mullapudi, S. / Bishop, E. / Tous, G. / Casas-Finet, J. / Hakki, F. / Strouse, R. / Schenerman, M.
#1: Journal: Patent / Year: 2005
Title: Crystals and structure of Synagis Fab
Authors: Braden, B. / Johnson, L.S.
History
DepositionAug 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Sep 18, 2013Group: Source and taxonomy
Revision 1.3Feb 5, 2014Group: Source and taxonomy
Revision 1.4Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.pdbx_database_id_patent / _citation.title / _citation_author.citation_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Immunoglobulin Fab light chain
H: Immunoglobulin Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,4242
Polymers47,4242
Non-polymers00
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-24 kcal/mol
Surface area19280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.106, 105.925, 69.404
Angle α, β, γ (deg.)90., 90., 90.
Int Tables number19
Space group name H-MP212121
DetailsFab heterodimer of antibody light chain and heavy chain variable and constant domain 1

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Components

#1: Antibody Immunoglobulin Fab light chain


Mass: 23177.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Humanized mouse antibody MEDI-493 Anti-respiratory syncytial virus antibody
Source: (gene. exp.) Homo sapiens, Mus musculus
#2: Antibody Immunoglobulin Fab heavy chain


Mass: 24246.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Humanized mouse antibody MEDI-493 Anti-respiratory syncytial virus antibody
Source: (gene. exp.) Homo sapiens, Mus musculus
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.99 Å3/Da / Density % sol: 58.82 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→6 Å / Num. obs: 33200 / Observed criterion σ(F): 2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→6 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection
all0.1936 -
obs-33200
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 0 357 3664
LS refinement shellResolution: 1.8→1.9 Å /
RfactorNum. reflection
Rwork0.251 -
obs-33200

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