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

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Basic information

Entry
Database: PDB / ID: 2qqq
TitleCrystal Structure of Novel Immune-Type Receptor 11 Extracellular Fragment from Ictalurus punctatus
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-like ...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: 1.98 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 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)51,3704
Polymers51,3704
Non-polymers00
Water10,269570
1
A: Novel immune-type receptor 11
B: Novel immune-type receptor 11


Theoretical massNumber of molelcules
Total (without water)25,6852
Polymers25,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
MethodPISA
2
C: Novel immune-type receptor 11
D: Novel immune-type receptor 11


Theoretical massNumber of molelcules
Total (without water)25,6852
Polymers25,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.446, 68.570, 99.129
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 2 biological units in the asymmetric unit (chains A & B and chains C & D).

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Components

#1: Protein
Novel immune-type receptor 11


Mass: 12842.494 Da / Num. of mol.: 4 / Fragment: Extracellular domain / Source method: isolated from a natural source / Source: (natural) Ictalurus punctatus (channel catfish) / References: UniProt: Q8UWK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 41.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Sodium Acetate Trihydrate, 0.1M Tris Hydrochloride, PEG 4000, 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: 1.98→30 Å / Num. all: 28785 / Num. obs: 28785 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.034 / Χ2: 1.015 / Net I/σ(I): 15.8
Reflection shellResolution: 1.98→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.087 / Num. unique all: 620 / Χ2: 0.577 / % possible all: 82.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→30 Å / FOM work R set: 0.782 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1474 4.8 %Random
Rwork0.202 ---
obs0.202 28785 93.3 %-
all-28785 --
Solvent computationBsol: 42.291 Å2
Displacement parametersBiso mean: 36.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.916 Å20 Å20 Å2
2---0.231 Å20 Å2
3----0.685 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 0 570 4114
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.1081.5
X-RAY DIFFRACTIONc_scbond_it3.0712
X-RAY DIFFRACTIONc_mcangle_it3.1162
X-RAY DIFFRACTIONc_scangle_it4.3922.5
LS refinement shellResolution: 1.98→2.02 Å
RfactorNum. reflection% reflection
Rfree0.275 99 -
Rwork0.232 --
obs-1683 80.16 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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