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

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Basic information

Entry
Database: PDB / ID: 2coq
TitleStructure of new antigen receptor variable domain from sharks
Componentsnew antigen receptor variable domain
KeywordsIMMUNE SYSTEM / IG VNAR / NATURAL TYPE2 / 12A-9
Function / homology
Function and homology information


T cell receptor complex / peptide antigen binding
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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStreltsov, V.A. / Carmichael, J.A. / Nuttall, S.D.
CitationJournal: Protein Sci. / Year: 2005
Title: Structure of a shark IgNAR antibody variable domain and modeling of an early-developmental isotype.
Authors: Streltsov, V.A. / Carmichael, J.A. / Nuttall, S.D.
History
DepositionMay 18, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 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

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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)11,7941
Polymers11,7941
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.268, 68.324, 39.511
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 new antigen receptor variable domain


Mass: 11794.160 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: Q8JJ25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1M Chess PH9.5, 50% PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2004 / Details: RH COATED SI MIRROR
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→34.2 Å / Num. obs: 6336 / % possible obs: 98.55 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 15.2
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.977 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VER

1ver


Resolution: 2.1→34.2 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.365 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.309 / ESU R Free: 0.24 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28048 289 4.6 %RANDOM
Rwork0.21753 ---
all0.22042 6336 --
obs0.22042 6336 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20 Å2
2--2.14 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms823 0 0 140 963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022833
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9591125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.265107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34222.85735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82515149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.958159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02610
X-RAY DIFFRACTIONr_nbd_refined0.2660.2322
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.233
X-RAY DIFFRACTIONr_mcbond_it0.5271.5542
X-RAY DIFFRACTIONr_mcangle_it0.9112853
X-RAY DIFFRACTIONr_scbond_it1.5643326
X-RAY DIFFRACTIONr_scangle_it2.4434.5272
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 24 -
Rwork0.295 427 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 6.943 Å / Origin y: 24.536 Å / Origin z: 17.102 Å
111213212223313233
T-0.2387 Å20.0078 Å20.055 Å2--0.1713 Å20.0075 Å2---0.2552 Å2
L6.4455 °21.8703 °21.3388 °2-3.159 °20.1304 °2--3.4491 °2
S0.007 Å °0.4336 Å °0.2948 Å °-0.1442 Å °0.0471 Å °0.0051 Å °-0.1403 Å °0.0107 Å °-0.0541 Å °

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