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- PDB-3eba: CAbHul6 FGLW mutant (humanized) in complex with human lysozyme -

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Basic information

Entry
Database: PDB / ID: 3eba
TitleCAbHul6 FGLW mutant (humanized) in complex with human lysozyme
Components
  • CAbHul6
  • Lysozyme C
KeywordsIMMUNE SYSTEM/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / IMMUNOGLOBULIN / nanobody / humanization / AMYLOID FIBRIL formation inhibition / Amyloid / Antimicrobial / Bacteriolytic enzyme / Disease mutation / Glycosidase / Hydrolase / Polymorphism / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLoris, R. / Vincke, C. / Saerens, D. / Martinez-Rodriguez, S. / Muyldermans, S. / Conrath, K.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: General Strategy to Humanize a Camelid Single-domain Antibody and Identification of a Universal Humanized Nanobody Scaffold
Authors: Vincke, C. / Loris, R. / Saerens, D. / Martinez-Rodriguez, S. / Muyldermans, S. / Conrath, K.
History
DepositionAug 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAbHul6
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1488
Polymers28,5722
Non-polymers5766
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-74 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.670, 63.670, 119.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Antibody CAbHul6


Mass: 13851.210 Da / Num. of mol.: 1 / Mutation: E41G, R42L, G44W
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: Antibody Lysozyme C / 1 / 4-beta-N-acetylmuramidase C


Mass: 14720.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Aspergillu niger / References: UniProt: P61626, lysozyme
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNO DBREF WAS GIVEN FOR PROTEIN MOLECULE A SINCE THIS IMMUNOGLOBULIN HEAVY CHAIN HAS VARIABLE REGION ...NO DBREF WAS GIVEN FOR PROTEIN MOLECULE A SINCE THIS IMMUNOGLOBULIN HEAVY CHAIN HAS VARIABLE REGION (SEE GB ENTRY GI:7263678). THE SEQUENCE CONTAINS MUTATIONS AS E41G, R42L AND G44W.

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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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.909 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 23285 / Num. obs: 23285 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 14.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2320 / Rsym value: 0.402 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1op9

1op9


Resolution: 1.85→14.82 Å
Isotropic thermal model: individual isotropic atomic B-factors
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: used anisotropi B-factor correction and bulk solvent correction from CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1833 -random
Rwork0.211 ---
all-23285 --
obs-23285 99.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.643 Å20 Å20 Å2
2---0.643 Å20 Å2
3---1.286 Å2
Refinement stepCycle: LAST / Resolution: 1.85→14.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 30 219 2178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0058
X-RAY DIFFRACTIONc_angle_deg1.325

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