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- PDB-1zmy: cAbBCII-10 VHH framework with CDR loops of cAbLys3 grafted on it ... -

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Basic information

Entry
Database: PDB / ID: 1zmy
TitlecAbBCII-10 VHH framework with CDR loops of cAbLys3 grafted on it and in complex with hen egg white lysozyme
Components
  • Antibody cabbcII-10:lys3
  • Lysozyme C
KeywordsIMMUNE SYSTEM/HYDROLASE / VHH / antibody / immune system / CDR grafting / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCamelus dromedarius (Arabian camel)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSaerens, D. / Pellis, M. / Loris, R. / Pardon, E. / Dumoulin, M. / Matagne, A. / Wyns, L. / Muyldermans, S. / Conrath, K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Identification of a universal VHH framework to graft non-canonical antigen-binding loops of camel single-domain antibodies
Authors: Saerens, D. / Pellis, M. / Loris, R. / Pardon, E. / Dumoulin, M. / Matagne, A. / Wyns, L. / Muyldermans, S. / Conrath, K.
History
DepositionMay 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody cabbcII-10:lys3
L: Lysozyme C
M: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)43,8773
Polymers43,8773
Non-polymers00
Water90150
1
A: Antibody cabbcII-10:lys3
L: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)29,5462
Polymers29,5462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-9 kcal/mol
Surface area11100 Å2
MethodPISA
2
M: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.331, 132.331, 63.397
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Cell settinghexagonal
Space group name H-MP65
DetailsThe assymetric unit contains one VHH:lysozyme complex as well as one free lysozyme molecule

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Components

#1: Antibody Antibody cabbcII-10:lys3 / immunoglobulin heavy chain VHDJ region


Mass: 15214.724 Da / Num. of mol.: 1 / Fragment: N-terminus, 142 residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#2: Protein Lysozyme C / E.C.3.2.1.17 / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.56 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NaCl, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.83 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 3→18 Å / Num. all: 12811 / Num. obs: 12811 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.75 % / Rmerge(I) obs: 0.223 / Net I/σ(I): 11.8
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1270 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→18 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1041 8.1 %random
Rwork0.206 ---
all0.2061 12811 --
obs0.2061 12811 --
Refinement stepCycle: LAST / Resolution: 3→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 0 50 2975
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007378
X-RAY DIFFRACTIONc_angle_deg1.54387

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