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- PDB-1jto: Degenerate interfaces in antigen-antibody complexes -

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Basic information

Entry
Database: PDB / ID: 1jto
TitleDegenerate interfaces in antigen-antibody complexes
Components
  • Lysozyme
  • Vh Single-Domain Antibody
KeywordsAntibody / Hydrolase / immunoglobulin / heavy chain antibody / VHH / interface
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDecanniere, K. / Transue, T.R. / Desmyter, A. / Maes, D. / Muyldermans, S. / Wyns, L.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Degenerate interfaces in antigen-antibody complexes.
Authors: Decanniere, K. / Transue, T.R. / Desmyter, A. / Maes, D. / Muyldermans, S. / Wyns, L.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme
Authors: Desmyter, A. / Transue, T.R. / Ghahroudi, M.A. / Thi, M.H. / Poortmans, F. / Hamers, R. / Muyldermans, S. / Wyns, L.
History
DepositionAug 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vh Single-Domain Antibody
B: Vh Single-Domain Antibody
L: Lysozyme
M: Lysozyme


Theoretical massNumber of molelcules
Total (without water)59,9774
Polymers59,9774
Non-polymers00
Water88349
1
A: Vh Single-Domain Antibody
L: Lysozyme


Theoretical massNumber of molelcules
Total (without water)29,9882
Polymers29,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-7 kcal/mol
Surface area11310 Å2
MethodPISA
2
B: Vh Single-Domain Antibody
M: Lysozyme


Theoretical massNumber of molelcules
Total (without water)29,9882
Polymers29,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-8 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.680, 69.710, 113.680
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 Vh Single-Domain Antibody


Mass: 15657.090 Da / Num. of mol.: 2 / Fragment: VH domain fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pHEN1 / Production host: Escherichia coli (E. coli) / References: GenBank: 2392447
#2: Protein Lysozyme


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


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 8000, potassium phosphate, , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Msodium formate1reservoir
20.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1996
RadiationMonochromator: Graphite single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 17829 / Num. obs: 17829 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 6.1
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1170 / Rsym value: 0.42 / % possible all: 84.8
Reflection
*PLUS

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Processing

Software
NameVersionClassification
EnrafNoniusdata collection
SCALAdata scaling
AMoREphasing
CNSrefinement
ENRAFNONIUSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MEL

1mel


Resolution: 2.5→20 Å / Isotropic thermal model: Overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2397 1666 random
Rwork0.1732 --
all0.208 19435 -
obs0.208 17101 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.116 Å20 Å20 Å2
2--3.414 Å20 Å2
3---4.703 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 0 49 3997
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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