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- PDB-3b5t: Crystal Structure of Novel Immune-Type Receptor 10 Se-Met Extrace... -

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Basic information

Entry
Database: PDB / ID: 3b5t
TitleCrystal Structure of Novel Immune-Type Receptor 10 Se-Met Extracellular Fragment Mutant N30D
ComponentsNovel immune-type receptor 10
KeywordsIMMUNE SYSTEM RECEPTOR / Immunoglobulin Variable Domain-Like Beta-Sandwich / Immune-Type Receptor / IMMUNE SYSTEM
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 10
Similarity search - Component
Biological speciesIctalurus punctatus (channel catfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 16, 2013Group: Derived calculations / Source and taxonomy
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)65,4665
Polymers65,4665
Non-polymers00
Water14,502805
1
B: Novel immune-type receptor 10
E: Novel immune-type receptor 10


Theoretical massNumber of molelcules
Total (without water)26,1862
Polymers26,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-15 kcal/mol
Surface area11140 Å2
MethodPISA
2
C: Novel immune-type receptor 10
D: Novel immune-type receptor 10


Theoretical massNumber of molelcules
Total (without water)26,1862
Polymers26,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-16 kcal/mol
Surface area11260 Å2
MethodPISA
3
A: Novel immune-type receptor 10

A: Novel immune-type receptor 10


Theoretical massNumber of molelcules
Total (without water)26,1862
Polymers26,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2660 Å2
ΔGint-10 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.305, 90.305, 137.402
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
11A-210-

HOH

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Components

#1: Protein
Novel immune-type receptor 10


Mass: 13093.131 Da / Num. of mol.: 5 / Fragment: Extracellular fragment / Mutation: N30D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ictalurus punctatus (channel catfish) / 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.: 805 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Na Citrate, 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: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2007 / Details: Oxford Danfysik toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 10.5 / Number: 478586 / Rmerge(I) obs: 0.057 / Χ2: 1 / D res high: 1.75 Å / D res low: 30 Å / Num. obs: 66060 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.973099.910.0463.8346.7
4.745.9710010.0342.1287.1
4.154.7410010.0311.7567.2
3.774.1510010.0331.6057.3
3.53.7710010.0341.4997.3
3.293.510010.0361.3837.4
3.133.2910010.0391.267.4
2.993.1310010.0421.1987.4
2.882.9910010.0491.1327.4
2.782.8810010.0541.0897.4
2.692.7810010.0570.9767.4
2.612.6910010.0671.0687.4
2.542.6110010.0660.947.4
2.482.5410010.0680.967.4
2.432.4810010.0660.8457.4
2.372.4310010.0740.8297.5
2.332.3710010.0780.8427.4
2.282.3310010.0820.8227.4
2.242.2899.910.11.037.4
2.22.2410010.0940.8167.5
2.172.210010.0940.7747.4
2.142.1710010.0930.7517.4
2.12.1410010.1030.7497.4
2.072.110010.1190.777.4
2.052.0710010.1390.9467.4
2.022.0510010.130.7037.4
1.992.0210010.1380.6567.4
1.971.9910010.1450.6567.4
1.951.9710010.1490.6527.4
1.931.9510010.1780.6437.5
1.911.9310010.2130.8277.4
1.891.9110010.2210.6337.4
1.871.8910010.240.6447.4
1.851.8710010.2480.5927.4
1.831.8510010.2820.6257.4
1.811.8310010.3090.5947.3
1.81.8110010.340.5656.8
1.781.810010.3470.5656.4
1.761.7810010.360.5435.8
1.751.7610010.3830.555.4
ReflectionResolution: 1.75→30 Å / Num. all: 66060 / Num. obs: 66060 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.057 / Χ2: 0.995 / Net I/σ(I): 10.5
Reflection shellResolution: 1.75→1.76 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.383 / Num. unique all: 1628 / Χ2: 0.55 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→30 Å / FOM work R set: 0.817 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3339 5.1 %random
Rwork0.185 ---
all0.185 66060 --
obs0.185 65907 99.9 %-
Solvent computationBsol: 31.526 Å2
Displacement parametersBiso mean: 24.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å20 Å20 Å2
2--0.005 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4498 0 0 805 5303
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.6071.5
X-RAY DIFFRACTIONc_scbond_it3.0062
X-RAY DIFFRACTIONc_mcangle_it2.4882
X-RAY DIFFRACTIONc_scangle_it4.5612.5
LS refinement shellResolution: 1.75→1.794 Å
RfactorNum. reflection% reflection
Rfree0.291 234 -
Rwork0.222 --
obs-4556 100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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