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- PDB-1op9: Complex of human lysozyme with camelid VHH HL6 antibody fragment -

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Basic information

Entry
Database: PDB / ID: 1op9
TitleComplex of human lysozyme with camelid VHH HL6 antibody fragment
Components
  • HL6 camel VHH fragment
  • Lysozyme C
KeywordsHYDROLASE / antigen-antibody complex / immunoglobulin / amyloid fibril formation inhibition
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / 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 / tertiary granule lumen / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsDumoulin, M. / Last, A.M. / Desmyter, A. / Decanniere, K. / Canet, D. / Larsson, G. / Spencer, A. / Archer, D.B. / Sasse, J. / Muyldermans, S. ...Dumoulin, M. / Last, A.M. / Desmyter, A. / Decanniere, K. / Canet, D. / Larsson, G. / Spencer, A. / Archer, D.B. / Sasse, J. / Muyldermans, S. / Wyns, L. / Redfield, C. / Matagne, A. / Robinson, C.V. / Dobson, C.M.
CitationJournal: Nature / Year: 2003
Title: A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme
Authors: Dumoulin, M. / Last, A.M. / Desmyter, A. / Decanniere, K. / Canet, D. / Larsson, G. / Spencer, A. / Archer, D.B. / Sasse, J. / Muyldermans, S. / Wyns, L. / Redfield, C. / Matagne, A. / ...Authors: Dumoulin, M. / Last, A.M. / Desmyter, A. / Decanniere, K. / Canet, D. / Larsson, G. / Spencer, A. / Archer, D.B. / Sasse, J. / Muyldermans, S. / Wyns, L. / Redfield, C. / Matagne, A. / Robinson, C.V. / Dobson, C.M.
History
DepositionMar 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE No dbref was given for protein molecule A since this immunoglobulin heavy chain has ...SEQUENCE No dbref was given for protein molecule A since this immunoglobulin heavy chain has variable region see GB entry GI:7263678

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HL6 camel VHH fragment
B: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)27,7602
Polymers27,7602
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.611, 48.226, 66.605
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody HL6 camel VHH fragment


Mass: 13039.251 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#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) / Gene: LYZ OR LZM / Production host: Aspergillus niger (mold) / References: UniProt: P61626, lysozyme
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.07 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 % W/V PEG4000, 0.2M imidazole malate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 mMprotein1drop
220 %(w/v)PEG40001reservoir
30.2 Mimidazole-malate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. all: 20351 / Num. obs: 20015 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.8
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1857 / % possible all: 89

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: antibody: 1jto lysozyme: 133l

1jto

133l


Resolution: 1.86→31 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.238 1055 random
Rwork0.196 --
all0.197 20351 -
obs0.197 19296 -
Displacement parametersBiso mean: 16.9 Å2
Refinement stepCycle: LAST / Resolution: 1.86→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 0 207 2165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg0.023
X-RAY DIFFRACTIONr_gen_planes_refined0.02

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