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- PDB-1yzz: Humanized caban33 at room temperature -

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Basic information

Entry
Database: PDB / ID: 1yzz
TitleHumanized caban33 at room temperature
Componentsanti-VSG immunoglobulin heavy chain variable domain cAbAn33
KeywordsUNKNOWN FUNCTION / antibody / camel antibody / humanization
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. / Decanniere, K. / 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
DepositionMar 1, 2005Deposition 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 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 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
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.473, 52.473, 165.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
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.: 17 / 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: 1.96 Å3/Da / Density % sol: 36.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, ammonium sulphate, TRIS, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 9871 / Num. obs: 9871 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.46 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 24.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 14.63 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 3.8 / Num. unique all: 672 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YC8

1yc8


Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 593 -random
Rwork0.233 ---
all0.238 6871 --
obs0.238 6871 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 0 17 1655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.42091
X-RAY DIFFRACTIONc_bond_d0.007954

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