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- PDB-1ver: Structure of New Antigen Receptor variable domain from sharks -

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Basic information

Entry
Database: PDB / ID: 1ver
TitleStructure of New Antigen Receptor variable domain from sharks
ComponentsNew Antigen Receptor variable domain
KeywordsIMMUNE SYSTEM / IG VNAR / NATIVE / 12Y-1
Function / homology
Function and homology information


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 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 / MIR / Resolution: 2.82 Å
AuthorsStreltsov, V.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor
Authors: Streltsov, V.A. / Varghese, J.N. / Carmichael, J.A. / Irving, R.A. / Hudson, P.J. / Nuttall, S.D.
History
DepositionApr 5, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)12,2671
Polymers12,2671
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.259, 97.259, 65.228
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein New Antigen Receptor variable domain / VNAR


Mass: 12266.757 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) / References: UniProt: Q6X1E7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M BIS-TRIS PROPANE, 45% PPG P400, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2003 / 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: 2.82→69.01 Å / Num. obs: 3975 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 18.1
Reflection shellResolution: 2.82→2.9 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.8 / % possible all: 94.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MIR / Resolution: 2.82→6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.179 / SU ML: 0.288 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25391 153 4.4 %RANDOM
Rwork0.16588 ---
all0.16972 ---
obs0.16972 3353 99.29 %-
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: 40.21 Å2
Baniso -1Baniso -2Baniso -3
1-3.53 Å20 Å20 Å2
2--3.53 Å20 Å2
3----7.06 Å2
Refinement stepCycle: LAST / Resolution: 2.82→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms770 0 0 97 867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021780
X-RAY DIFFRACTIONr_bond_other_d0.0020.02710
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9551050
X-RAY DIFFRACTIONr_angle_other_deg0.83831648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.873598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02165
X-RAY DIFFRACTIONr_nbd_refined0.220.2147
X-RAY DIFFRACTIONr_nbd_other0.2240.2841
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.2558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.370.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3640.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3631.5488
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.692783
X-RAY DIFFRACTIONr_scbond_it1.0383292
X-RAY DIFFRACTIONr_scangle_it1.8644.5267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.82→2.877 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.543 11
Rwork0.339 195
Refinement TLS params.Method: refined / Origin x: 45.611 Å / Origin y: 36.411 Å / Origin z: 14.235 Å
111213212223313233
T0.0948 Å2-0.1415 Å2-0.1115 Å2-0.2124 Å20.1801 Å2--0.2758 Å2
L3.5582 °20.4045 °2-0.8273 °2-7.2854 °2-0.9129 °2--17.6513 °2
S0.1545 Å °-0.684 Å °-0.0196 Å °0.7097 Å °-0.6861 Å °-0.3902 Å °-0.408 Å °0.6079 Å °0.5316 Å °

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