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- PDB-2qte: Crystal Structure of Novel Immune-Type Receptor 11 Extracellular ... -

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Basic information

Entry
Database: PDB / ID: 2qte
TitleCrystal Structure of Novel Immune-Type Receptor 11 Extracellular Fragment Mutant N30D
ComponentsNovel immune-type receptor 11
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 11
Similarity search - Component
Biological speciesIctalurus punctatus (channel catfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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
DepositionAug 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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 1.4Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Novel immune-type receptor 11
B: Novel immune-type receptor 11
C: Novel immune-type receptor 11
D: Novel immune-type receptor 11


Theoretical massNumber of molelcules
Total (without water)51,3744
Polymers51,3744
Non-polymers00
Water10,935607
1
A: Novel immune-type receptor 11
B: Novel immune-type receptor 11


Theoretical massNumber of molelcules
Total (without water)25,6872
Polymers25,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
MethodPISA
2
C: Novel immune-type receptor 11
D: Novel immune-type receptor 11


Theoretical massNumber of molelcules
Total (without water)25,6872
Polymers25,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.476, 68.662, 99.632
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. There are two biological units in the asymmetric unit (chains A & B and chains D & C).

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Components

#1: Protein
Novel immune-type receptor 11


Mass: 12843.479 Da / Num. of mol.: 4 / Fragment: Extracellular fragment / Mutation: N30D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ictalurus punctatus (channel catfish) / Strain: wild type / Gene: NITR11 / Plasmid: pET-Blue1 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: Q8UWK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 0.2M Calcium Acetate hydrate, 0.1M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9322 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 / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 32478 / Num. obs: 32478 / % possible obs: 92 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.059 / Χ2: 0.996 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.16 / Num. unique all: 812 / Χ2: 0.751 / % possible all: 91.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→30 Å / FOM work R set: 0.796 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1621 4.6 %random
Rwork0.2 ---
all0.198 32420 --
obs0.198 32420 91.2 %-
Solvent computationBsol: 29.186 Å2
Displacement parametersBiso mean: 25.535 Å2
Baniso -1Baniso -2Baniso -3
1--0.239 Å20 Å20 Å2
2--0.082 Å20 Å2
3---0.157 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 0 607 4151
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.8511.5
X-RAY DIFFRACTIONc_scbond_it4.5872
X-RAY DIFFRACTIONc_mcangle_it3.8982
X-RAY DIFFRACTIONc_scangle_it6.0742.5
LS refinement shellResolution: 1.9→1.953 Å
RfactorNum. reflection% reflection
Rfree0.309 119 -
Rwork0.245 --
obs-2173 89.15 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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