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- PDB-2ywz: Structure of new antigen receptor variable domain from sharks -

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Basic information

Entry
Database: PDB / ID: 2ywz
TitleStructure of new antigen receptor variable domain from sharks
Componentsnew antigen receptor variable domain
KeywordsIMMUNE SYSTEM / IG VNAR / 1-A-11
Function / homology
Function and homology information


T cell receptor complex / peptide antigen binding / adaptive immune response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
New antigen receptor variable domain
Similarity search - Component
Biological speciesOrectolobus maculatus (spotted wobbegong)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsStreltsov, V.A.
CitationJournal: Proteins / Year: 2007
Title: Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures
Authors: Simmons, D.P. / Streltsov, V.A. / Dolezal, O. / Hudson, P.J. / Coley, A.M. / Foley, M. / Proll, D.F. / Nuttall, S.D.
History
DepositionApr 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence has been deposited to databasthe GB with accession code, DQ269923.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: new antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)12,1571
Polymers12,1571
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.252, 50.442, 46.731
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein new antigen receptor variable domain


Mass: 12157.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong)
Plasmid: pGC / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: A9CBG5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M CACODYLATE, 36% MPEG 2000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Aug 20, 2004 / Details: AXCO MICROCAPILLARY FOCUSING OPTICS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→18.11 Å / Num. obs: 6619 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.0084 / Rsym value: 0.0084 / Net I/σ(I): 21
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.55 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VES

1ves


Resolution: 2.21→18.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.421 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 315 4.8 %RANDOM
Rwork0.18526 ---
obs0.18853 6303 98.7 %-
all-6303 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.801 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å21.64 Å2
2--0.19 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.21→18.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 0 119 969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022866
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9641174
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1523.93933
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.4915152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.474155
X-RAY DIFFRACTIONr_chiral_restr0.1370.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02630
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2370
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2577
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7121.5560
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.292889
X-RAY DIFFRACTIONr_scbond_it1.8823352
X-RAY DIFFRACTIONr_scangle_it3.1824.5285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.205→2.261 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 23
Rwork0.235 434

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