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- PDB-1yc8: cAbAn33- Y37V/E44G/R45L triple mutant -

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Basic information

Entry
Database: PDB / ID: 1yc8
TitlecAbAn33- Y37V/E44G/R45L triple mutant
Componentsanti-VSG immunoglobulin heavy chain variable domain cAbAn33
KeywordsIMMUNE SYSTEM / antibody / camel antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsConrath, K. / Vincke, C. / Stijlemans, B. / Schymkowitz, J. / Wyns, L. / Muyldermans, S. / Loris, R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Antigen Binding and Solubility Effects upon the Veneering of a Camel VHH in Framework-2 to Mimic a VH.
Authors: Conrath, K. / Vincke, C. / Stijlemans, B. / Schymkowitz, J. / Decanniere, K. / Wyns, L. / Muyldermans, S. / Loris, R.
History
DepositionDec 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 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: anti-VSG immunoglobulin heavy chain variable domain cAbAn33
B: anti-VSG immunoglobulin heavy chain variable domain cAbAn33


Theoretical massNumber of molelcules
Total (without water)27,2302
Polymers27,2302
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.843, 51.843, 164.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody anti-VSG immunoglobulin heavy chain variable domain cAbAn33


Mass: 13615.040 Da / Num. of mol.: 2 / Fragment: cAbAn33-hu / Mutation: Y37V/E44G/R45L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) / References: GenBank: 30350899
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-3350, ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 6709 / Num. obs: 6709 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.4
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 3.2 / Num. unique all: 642 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: cAbAn33 (pdb entry 1YC7)

1yc7


Resolution: 2.7→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.324 558 random
Rwork0.246 --
all0.253 6127 -
obs0.253 6127 -
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 0 40 1675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007471
X-RAY DIFFRACTIONc_angle_deg1.56229

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