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- PDB-4q9c: IgNAR antibody domain C3 -

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Basic information

Entry
Database: PDB / ID: 4q9c
TitleIgNAR antibody domain C3
ComponentsNovel antigen receptor
KeywordsIMMUNE SYSTEM / protein evolution / antibody structure / protein folding
Function / homology
Function and homology information


Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Novel antigen receptor
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFeige, J.M. / Graewert, M.A. / Marcinowski, M. / Hennig, J. / Behnke, J. / Auslaender, D. / Herold, E.M. / Peschek, J. / Castro, C.D. / Flajnik, M.F. ...Feige, J.M. / Graewert, M.A. / Marcinowski, M. / Hennig, J. / Behnke, J. / Auslaender, D. / Herold, E.M. / Peschek, J. / Castro, C.D. / Flajnik, M.F. / Hendershot, L.M. / Sattler, M. / Groll, M. / Buchner, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins.
Authors: Feige, M.J. / Grawert, M.A. / Marcinowski, M. / Hennig, J. / Behnke, J. / Auslander, D. / Herold, E.M. / Peschek, J. / Castro, C.D. / Flajnik, M. / Hendershot, L.M. / Sattler, M. / Groll, M. / Buchner, J.
History
DepositionApr 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Novel antigen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7266
Polymers12,2441
Non-polymers4825
Water21612
1
A: Novel antigen receptor
hetero molecules

A: Novel antigen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,45212
Polymers24,4882
Non-polymers96510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_654-x+y+1,y,-z-1/21
Buried area3760 Å2
ΔGint-65 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.148, 99.148, 52.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1004-

HOH

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Components

#1: Protein Novel antigen receptor / IgNAR antibody


Mass: 12243.794 Da / Num. of mol.: 1 / Fragment: domain C3 (UNP residues 343-452)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q90544
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.0 M lithium chloride, 0.1 M citric acid, 20% PEG6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.514 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: Bruker AXS Microstar optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 4052 / Num. obs: 4052 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 22.5
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q97

4q97


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.88 / SU B: 30.862 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2872 182 4.5 %RANDOM
Rwork0.25851 ---
obs0.25975 3851 99.63 %-
all-4033 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.408 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å21.4 Å20 Å2
2--1.4 Å20 Å2
3----4.53 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 25 12 853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02856
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.9821162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8495104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71924.06332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55115139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.545155
X-RAY DIFFRACTIONr_chiral_restr0.0550.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022618
X-RAY DIFFRACTIONr_rigid_bond_restr1.1413854
X-RAY DIFFRACTIONr_sphericity_free27.60453
X-RAY DIFFRACTIONr_sphericity_bonded11.0445850
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 12 -
Rwork0.344 264 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 40.7233 Å / Origin y: -6.2609 Å / Origin z: -12.0218 Å
111213212223313233
T0.0078 Å2-0.0025 Å2-0.0019 Å2-0.0086 Å2-0.0046 Å2--0.0105 Å2
L0.0533 °2-0.0693 °20.0173 °2-0.3923 °2-0.211 °2--0.2219 °2
S-0.0135 Å °-0.0037 Å °0.0008 Å °-0.006 Å °0.031 Å °0.0246 Å °-0.0059 Å °-0.0089 Å °-0.0175 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A345 - 449
2X-RAY DIFFRACTION1A901 - 902

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