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

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Basic information

Entry
Database: PDB / ID: 2ywy
TitleStructure of new antigen receptor variable domain from sharks
Componentsnew antigen receptor variable domain
KeywordsIMMUNE SYSTEM / IG VNAR / 1-A-7
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: 2.71 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: Advisory / 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence has been deposited to databasthe GB with accession code, DQ269922.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: new antigen receptor variable domain
B: new antigen receptor variable domain
C: new antigen receptor variable domain
D: new antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)49,5834
Polymers49,5834
Non-polymers00
Water6,413356
1
A: new antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)12,3961
Polymers12,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: new antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)12,3961
Polymers12,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: new antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)12,3961
Polymers12,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: new antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)12,3961
Polymers12,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.498, 88.661, 101.754
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: Protein
new antigen receptor variable domain


Mass: 12395.760 Da / Num. of mol.: 4
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: A9CBG4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M ACETATE, 20% PEP (17/8 PO/OH), pH 4.60, 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 5, 2004 / Details: AXCO MICROCAPILLARY FOCUSING OPTICS
RadiationMonochromator: NO / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→21.57 Å / Num. obs: 19373 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.0119 / Rsym value: 0.0119 / Net I/σ(I): 7.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.6 / % possible all: 87.6

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VES

1ves


Resolution: 2.71→21.57 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.873 / SU B: 21.432 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.6 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1969 10.2 %RANDOM
Rwork0.18 ---
obs0.189 17386 94.8 %-
all-17386 --
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: 62.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.71→21.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 0 356 3672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9534548
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9835426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86623.611144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27315586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4131528
X-RAY DIFFRACTIONr_chiral_restr0.1020.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022492
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.21504
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22235
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.52159
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18523406
X-RAY DIFFRACTIONr_scbond_it1.83731373
X-RAY DIFFRACTIONr_scangle_it3.0854.51142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 110 -
Rwork0.272 1048 -
obs--78.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.3342-2.5042-0.15777.5816-2.90743.4203-0.1711-0.0682-0.33330.49930.16440.05320.4185-0.05850.00670.125-0.01940.0521-0.4287-0.0228-0.34642.6422.71111.285
22.74543.5073-0.74139.0661-1.73014.19550.0718-0.1741-0.04820.44410.1187-0.13240.1746-0.1788-0.1906-0.08590.03080.0296-0.4207-0.0445-0.288857.28823.2719.555
32.98642.1246-0.27589.99533.28647.5785-0.1650.02210.21340.33360.3434-0.3049-0.14770.2998-0.1784-0.0640.0309-0.0168-0.39570.0362-0.273825.80622.82123.052
42.92452.051-0.085611.8456-3.14764.9578-0.23430.15730.01070.31980.2862-0.2265-0.2099-0.0112-0.05190.02440.06210.0373-0.40090.0323-0.3619.7282.52136.875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1111 - 111
2X-RAY DIFFRACTION2BB1 - 1111 - 111
3X-RAY DIFFRACTION3CC1 - 1111 - 111
4X-RAY DIFFRACTION4DD1 - 1111 - 111

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