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- PDB-1sq2: Crystal Structure Analysis of the Nurse Shark New Antigen Recepto... -

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Basic information

Entry
Database: PDB / ID: 1sq2
TitleCrystal Structure Analysis of the Nurse Shark New Antigen Receptor (NAR) Variable Domain in Complex With Lysozyme
Components
  • Lysozyme C
  • novel antigen receptor
KeywordsHYDROLASE/IMMUNE SYSTEM / immunoglobulin fold / protein-protein complex / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


T cell receptor complex / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / peptide antigen binding / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium ...T cell receptor complex / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / peptide antigen binding / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / adaptive immune response / 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 / Immunoglobulin V-Type ...: / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Lysozyme C / Novel antigen receptor
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsStanfield, R.L. / Dooley, H. / Flajnik, M.F. / Wilson, I.A.
CitationJournal: Science / Year: 2004
Title: Crystal structure of a shark single-domain antibody V region in complex with lysozyme.
Authors: Stanfield, R.L. / Dooley, H. / Flajnik, M.F. / Wilson, I.A.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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
L: Lysozyme C
N: novel antigen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7328
Polymers26,3862
Non-polymers3466
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-9 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.02, 109.84, 29.28
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hen egg white / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Protein novel antigen receptor


Mass: 12055.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Plasmid: pIMS100 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q8AXI4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG 10,000, 0.1M imidazole HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.45→35 Å / Num. all: 40482 / Num. obs: 40482 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.054 / Net I/σ(I): 37.9
Reflection shellResolution: 1.45→1.48 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.394 / % possible all: 52.6

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1LKS AND 1QLE (residues 1-85)

1lks

1qle


Resolution: 1.45→35 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.701 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.077 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22534 2025 5 %RANDOM
Rwork0.19601 ---
obs0.19744 40410 93.16 %-
all-40410 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.45→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 21 189 2045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211887
X-RAY DIFFRACTIONr_bond_other_d0.0030.021649
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9282541
X-RAY DIFFRACTIONr_angle_other_deg0.93833819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1823.10387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58815306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4991519
X-RAY DIFFRACTIONr_chiral_restr0.1230.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
X-RAY DIFFRACTIONr_nbd_refined0.2290.2355
X-RAY DIFFRACTIONr_nbd_other0.20.21680
X-RAY DIFFRACTIONr_nbtor_other0.0840.21181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2120
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.221
X-RAY DIFFRACTIONr_mcbond_it1.6151.51509
X-RAY DIFFRACTIONr_mcbond_other0.3561.5510
X-RAY DIFFRACTIONr_mcangle_it1.95721872
X-RAY DIFFRACTIONr_scbond_it2.8753848
X-RAY DIFFRACTIONr_scangle_it3.8354.5669
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 -
Rwork0.308 1645

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