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- PDB-1yc7: cAbAn33 VHH fragment against VSG -

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Basic information

Entry
Database: PDB / ID: 1yc7
TitlecAbAn33 VHH fragment against VSG
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: 1.6 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_sheet / struct_site
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 / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7824
Polymers27,5902
Non-polymers1922
Water5,080282
1
A: anti-VSG immunoglobulin heavy chain variable domain cAbAn33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8912
Polymers13,7951
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: anti-VSG immunoglobulin heavy chain variable domain cAbAn33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8912
Polymers13,7951
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.993, 91.600, 82.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13795.182 Da / Num. of mol.: 2 / Fragment: cAbAn33
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-4000, ammomium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 27, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 31676 / Num. obs: 31676 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.69 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2802 / % possible all: 86.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.212 2554 random
Rwork0.192 --
all0.194 31676 -
obs0.194 31676 -
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 10 282 2000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008192
X-RAY DIFFRACTIONc_angle_deg1.50964

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