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- PDB-2qjd: Crystal Structure of Novel Immune-Type Receptor 10 Extracellular ... -

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Basic information

Entry
Database: PDB / ID: 2qjd
TitleCrystal Structure of Novel Immune-Type Receptor 10 Extracellular Fragment Mutant N30D
ComponentsNovel immune-type receptor 10
KeywordsIMMUNE SYSTEM / Immunoglobulin Variable Domain-Like Beta-Sandwich / Immune-Type Receptor
Function / homology
Function and homology information


response to bacterium / membrane
Similarity search - Function
: / 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-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
Novel immune-type receptor 10
Similarity search - Component
Biological speciesIctalurus punctatus (channel catfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsOstrov, D.A. / Hernandez Prada, J.A. / Haire, R.N. / Cannon, J.P. / Magis, A.T. / Bailey, K.M. / Litman, G.W.
CitationJournal: Immunity / Year: 2008
Title: A bony fish immunological receptor of the NITR multigene family mediates allogeneic recognition.
Authors: Cannon, J.P. / Haire, R.N. / Magis, A.T. / Eason, D.D. / Winfrey, K.N. / Hernandez Prada, J.A. / Bailey, K.M. / Jakoncic, J. / Litman, G.W. / Ostrov, D.A.
History
DepositionJul 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Novel immune-type receptor 10
B: Novel immune-type receptor 10


Theoretical massNumber of molelcules
Total (without water)25,5812
Polymers25,5812
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-13.8 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.952, 94.952, 67.668
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsThe biological unit is a dimer. There is 1 biological unit in the asymmetric unit (chains A & B).

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Components

#1: Protein Novel immune-type receptor 10


Mass: 12790.462 Da / Num. of mol.: 2 / Fragment: Extracellular fragment / Mutation: N30D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ictalurus punctatus (channel catfish) / Strain: wild type / Gene: NITR10 / Plasmid: pET-Blue1 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: Q8UWK5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.44 Å3/Da / Density % sol: 64.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 4000, 0.08M Tris HCL, 0.16M Magnesium Chloride, 20% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 27, 2007 / Details: Oxford Danfysik toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.44→30 Å / Num. all: 13266 / Num. obs: 13266 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.071 / Χ2: 1.097 / Net I/σ(I): 10.1
Reflection shellResolution: 2.44→2.46 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.368 / Num. unique all: 262 / Χ2: 0.896 / % possible all: 80.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→28.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.483 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 651 4.9 %RANDOM
Rwork0.184 ---
all0.185 13266 --
obs0.186 13252 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.44→28.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 0 144 1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221818
X-RAY DIFFRACTIONr_angle_refined_deg2.2691.9382430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0685216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97623.8394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.37515340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6731512
X-RAY DIFFRACTIONr_chiral_restr0.170.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021386
X-RAY DIFFRACTIONr_nbd_refined0.2330.2780
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.211
X-RAY DIFFRACTIONr_mcbond_it1.5531.51106
X-RAY DIFFRACTIONr_mcangle_it2.62721722
X-RAY DIFFRACTIONr_scbond_it3.5843821
X-RAY DIFFRACTIONr_scangle_it5.9074.5708
LS refinement shellResolution: 2.439→2.502 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 37 -
Rwork0.246 820 -
obs-857 87.36 %

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