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

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Basic information

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


immune system process / response to bacterium / plasma 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 / Immunoglobulin-like fold / Immunoglobulins ...: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / 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 / SAD / Resolution: 1.56 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 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Novel immune-type receptor 10
B: Novel immune-type receptor 10
C: Novel immune-type receptor 10
D: Novel immune-type receptor 10
E: Novel immune-type receptor 10


Theoretical massNumber of molelcules
Total (without water)64,5335
Polymers64,5335
Non-polymers00
Water14,304794
1
B: Novel immune-type receptor 10

B: Novel immune-type receptor 10


Theoretical massNumber of molelcules
Total (without water)25,8132
Polymers25,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2700 Å2
ΔGint-15 kcal/mol
Surface area11460 Å2
MethodPISA
2
A: Novel immune-type receptor 10
D: Novel immune-type receptor 10


Theoretical massNumber of molelcules
Total (without water)25,8132
Polymers25,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-15 kcal/mol
Surface area11360 Å2
MethodPISA
3
C: Novel immune-type receptor 10
E: Novel immune-type receptor 10


Theoretical massNumber of molelcules
Total (without water)25,8132
Polymers25,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-14 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.246, 90.246, 136.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-336-

HOH

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Components

#1: Protein
Novel immune-type receptor 10


Mass: 12906.536 Da / Num. of mol.: 5 / Fragment: Extracellular / Source method: isolated from a natural source / Details: Channel catfish / Source: (natural) Ictalurus punctatus (channel catfish) / References: UniProt: Q8UWK5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5M Na Citrate, pH 8.0, 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 / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.56→30 Å / Num. all: 91403 / Num. obs: 91403 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.047 / Χ2: 0.992 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.56-1.573.60.4621320.67895.6
1.57-1.594.20.44622480.68597.8
1.59-1.64.90.4522350.65299.4
1.6-1.625.60.44422600.65599.6
1.62-1.636.20.42422500.669100
1.63-1.656.60.39722940.71899.8
1.65-1.6670.38922640.687100
1.66-1.687.20.36622590.7399.8
1.68-1.77.20.36422800.709100
1.7-1.727.40.31522670.69299.8
1.72-1.747.20.27922720.6999.9
1.74-1.767.40.25822730.71100
1.76-1.787.30.23922810.71799.9
1.78-1.87.30.21722590.73100
1.8-1.827.40.18522650.74100
1.82-1.857.30.16322770.773100
1.85-1.887.40.15422850.838100
1.88-1.97.40.13322850.826100
1.9-1.937.40.1222580.84100
1.93-1.977.40.10323160.887100
1.97-27.40.09722640.915100
2-2.047.40.08522800.917100
2.04-2.077.40.0822920.941100
2.07-2.127.40.07223000.962100
2.12-2.167.40.06522620.976100
2.16-2.217.40.06323191.003100
2.21-2.277.40.05922820.986100
2.27-2.337.40.05822941.016100
2.33-2.47.40.05322841.023100
2.4-2.487.40.05123141.073100
2.48-2.567.30.04722971.142100
2.56-2.677.40.04823121.134100
2.67-2.797.40.04422921.20899.9
2.79-2.947.40.04123081.31399.9
2.94-3.127.30.03623231.44299.7
3.12-3.367.30.03423181.56499.7
3.36-3.77.30.03223341.63899.7
3.7-4.237.20.03123431.70599.3
4.23-5.337.10.02923651.60298.7
5.33-306.70.03323601.81494.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å29.63 Å
Translation3 Å29.63 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.56→30 Å / FOM work R set: 0.791 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4587 5 %Random
Rwork0.196 ---
all-91403 --
obs-91335 99.5 %-
Solvent computationBsol: 29.816 Å2
Displacement parametersBiso mean: 26.141 Å2
Baniso -1Baniso -2Baniso -3
1--0.159 Å20 Å20 Å2
2---0.159 Å20 Å2
3---0.318 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.56→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 0 794 5284
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.0081.5
X-RAY DIFFRACTIONc_scbond_it3.6052
X-RAY DIFFRACTIONc_mcangle_it2.8572
X-RAY DIFFRACTIONc_scangle_it5.3052.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.56-1.570.273830.25615771660
1.57-1.580.269850.25317011786
1.58-1.590.313860.23716571743
1.59-1.60.269810.24117621843
1.6-1.620.273940.23316991793
1.62-1.630.24980.22817231821
1.63-1.640.259840.21517271811
1.64-1.650.2611000.20916971797
1.65-1.670.248910.22917301821
1.67-1.680.237810.21317231804
1.68-1.690.2421060.22417081814
1.69-1.710.279770.21517481825
1.71-1.720.229840.21617171801
1.72-1.740.26880.20717941882
1.74-1.760.223770.20117091786
1.76-1.770.2271020.21317171819
1.77-1.790.248950.20417071802
1.79-1.810.23890.2117291818
1.81-1.830.257910.20217291820
1.83-1.850.285850.20717461831
1.85-1.870.262890.20717471836
1.87-1.890.273820.20417191801
1.89-1.920.25930.2117371830
1.92-1.940.21920.19817381830
1.94-1.970.255990.19617391838
1.97-1.990.249920.19217271819
1.99-2.020.232790.19617411820
2.02-2.050.239990.19917511850
2.05-2.080.291900.20117061796
2.08-2.120.196950.19917581853
2.12-2.150.242950.19817261821
2.15-2.190.211870.19717371824
2.19-2.230.219940.19717541848
2.23-2.280.233950.19517261821
2.28-2.330.2111010.217401841
2.33-2.380.2391100.20317391849
2.38-2.440.2321000.20917351835
2.44-2.510.2351010.20717241825
2.51-2.580.244900.20717511841
2.58-2.670.242980.21717561854
2.67-2.760.253690.22217651834
2.76-2.870.237940.21617601854
2.87-30.194850.20217641849
3-3.160.22870.18117561843
3.16-3.360.224980.17717651863
3.36-3.620.21990.16517761875
3.62-3.980.166920.15217681860
3.98-4.560.164950.15317811876
4.56-5.730.1831080.16617811889
5.73-300.2461020.2617811883
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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