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- PDB-2if7: Crystal Structure of NTB-A -

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Basic information

Entry
Database: PDB / ID: 2if7
TitleCrystal Structure of NTB-A
ComponentsSLAM family member 6
KeywordsIMMUNE SYSTEM / NTB-A / SLAM6 / LY108 / Homophilic receptor
Function / homology
Function and homology information


T-helper 17 cell lineage commitment / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-17 production / regulation of immune response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / membrane => GO:0016020 / innate immune response / extracellular exosome / 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 / 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
SLAM family member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsCao, E. / Ramagopal, U.A. / Fedorov, A.A. / Fedorov, E.V. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Immunity / Year: 2006
Title: NTB-A Receptor Crystal Structure: Insights into Homophilic Interactions in the Signaling Lymphocytic Activation Molecule Receptor Family.
Authors: Cao, E. / Ramagopal, U.A. / Fedorov, A. / Fedorov, E. / Yan, Q. / Lary, J.W. / Cole, J.L. / Nathenson, S.G. / Almo, S.C.
History
DepositionSep 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Remark 600Heterogen Authors state that it is difficult to assign CL and CA ions at 3.00 ANGSTROMS resolution. ...Heterogen Authors state that it is difficult to assign CL and CA ions at 3.00 ANGSTROMS resolution. Therefore, the identities of these ions are ambiguous in the PDB file.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SLAM family member 6
B: SLAM family member 6
C: SLAM family member 6
D: SLAM family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8577
Polymers86,7424
Non-polymers1163
Water543
1
A: SLAM family member 6
B: SLAM family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4113
Polymers43,3712
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-19 kcal/mol
Surface area21310 Å2
MethodPISA
2
C: SLAM family member 6
D: SLAM family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4464
Polymers43,3712
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-10 kcal/mol
Surface area21510 Å2
MethodPISA
3
C: SLAM family member 6
D: SLAM family member 6
hetero molecules

C: SLAM family member 6
D: SLAM family member 6
hetero molecules

A: SLAM family member 6
B: SLAM family member 6
hetero molecules

A: SLAM family member 6
B: SLAM family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,71414
Polymers173,4838
Non-polymers2316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
crystal symmetry operation3_546x+1/2,y-1/2,z+11
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area11380 Å2
ΔGint-97 kcal/mol
Surface area80920 Å2
MethodPISA
4
C: SLAM family member 6
D: SLAM family member 6
hetero molecules

A: SLAM family member 6
B: SLAM family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8577
Polymers86,7424
Non-polymers1163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area4300 Å2
ΔGint-44 kcal/mol
Surface area41850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.196, 148.452, 86.572
Angle α, β, γ (deg.)90.000, 112.860, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a dimer.There are two biological units in the asymmetric unit (chains A, B and C, D)

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Components

#1: Protein
SLAM family member 6 / NK-T-B-antigen / NTB-A / Activating NK receptor


Mass: 21685.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLAMF6, KALI / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta (DE3) pLysS / References: UniProt: Q96DU3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.13 Å3/Da / Density % sol: 70.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.4-0.5 M CaCl2, 0.1 M HEPES pH 7.4, 1.0 mM Pt(NH3)2Cl2, 4% PEG-400, Vapor diffusion, Sitting drop, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789,0.9791,0.9714
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97911
30.97141
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
2.5111.51110800.061.073.24472798.6
2.429979910.0761.023.34136098.9
2.538.41106750.081.043.194503997.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.895099.310.0321.4352.5
5.476.8999.510.0451.2532.5
4.785.4799.610.0421.162.5
4.344.7899.610.0491.1632.5
4.034.3499.510.0661.0892.5
3.794.0399.410.0980.9942.5
3.63.7999.410.1340.9522.5
3.453.699.310.1950.9222.5
3.313.4599.210.2830.8482.4
3.23.3191.110.3960.8112.4
7.15099.120.0371.4342.4
5.647.199.620.0551.1372.4
4.935.6499.420.0571.1222.4
4.484.9399.620.0651.0912.4
4.164.4899.520.0841.0792.4
3.914.1699.420.1280.9412.4
3.723.9199.220.1740.9042.3
3.553.7299.220.2490.8692.4
3.423.5598.620.3570.8712.3
3.33.4295.420.5180.7672.3
6.875099.330.0411.5752.5
5.456.8799.630.0561.1622.5
4.765.4599.530.0571.1532.5
4.334.7699.530.0661.1262.5
4.024.3399.530.0951.0482.5
3.784.0299.430.1460.9372.5
3.593.7899.330.2010.9082.5
3.443.5998.830.30.8552.5
3.33.4496.230.4440.7912.4
3.193.383.230.590.7582.2
ReflectionResolution: 3→40 Å / Num. all: 28402 / Num. obs: 28402 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.048 / Χ2: 0.969 / Net I/σ(I): 15.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.08 / Num. unique all: 2838 / Rsym value: 0.303 / Χ2: 0.694 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
Cootmodel building
Omodel building
RefinementMethod to determine structure: MAD / Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.888 / SU B: 33.639 / SU ML: 0.31 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.939 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1413 5 %RANDOM
Rwork0.213 ---
all0.216 28151 --
obs0.216 28151 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.603 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å20 Å23.14 Å2
2---1.44 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5960 0 3 3 5966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226080
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9538271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3525.273275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.258151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4131528
X-RAY DIFFRACTIONr_chiral_restr0.0680.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024530
X-RAY DIFFRACTIONr_nbd_refined0.2990.22555
X-RAY DIFFRACTIONr_nbtor_refined0.3320.24140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2211
X-RAY DIFFRACTIONr_metal_ion_refined0.1640.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2390.22
X-RAY DIFFRACTIONr_mcbond_it1.0041.53851
X-RAY DIFFRACTIONr_mcangle_it1.79326180
X-RAY DIFFRACTIONr_scbond_it2.51732458
X-RAY DIFFRACTIONr_scangle_it4.2394.52091
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 102 -
Rwork0.289 1945 -
obs-2047 99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4853-0.9916-1.278412.2341-3.40094.83310.02190.0957-0.2976-0.2271-0.084-0.119-0.13070.06660.0621-0.51560.0249-0.0708-0.5229-0.0862-0.100448.196260.17711.5016
27.73754.0419-0.36939.70350.03834.33920.3005-0.49550.19460.92-0.28350.56120.2262-0.6307-0.017-0.4111-0.01540.0657-0.3986-0.0257-0.366236.360920.115612.0072
314.6242-4.6078-4.25896.6586-0.46325.124-0.355-0.83890.15030.55320.4161-0.5489-0.26430.401-0.0611-0.12070.1722-0.0398-0.4679-0.0172-0.163141.427278.052410.5222
49.2185-0.2364-0.67412.3797-0.95225.1436-0.1009-0.8427-0.46550.14290.00050.18220.2489-0.38160.1004-0.24970.0828-0.0207-0.2190.1744-0.28960.964688.907725.7879
57.3255-1.0376-1.68256.27482.62064.90630.21720.69840.7454-1.4514-0.19130.1118-0.43340.0263-0.0260.66540.117-0.19220.45130.49250.43092.304252.480626.8806
65.19273.2320.42692.31881.76717.3740.3213-1.4598-0.06411.3982-0.43730.33350.28290.11420.1160.11620.0751-0.0540.57230.12680.1871-1.048191.60944.9242
78.4242-3.61114.03596.6152-2.57269.76680.41570.77650.0028-1.2674-0.25560.86270.7336-0.5068-0.16010.1656-0.0168-0.16760.15340.16050.08510.704633.977236.7286
85.34640.67191.05792.1050.70674.9254-0.09460.11910.2298-0.1145-0.03420.0259-0.069-0.12170.1288-0.5056-0.00610.0212-0.6952-0.0463-0.454615.824322.249477.2359
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 1045 - 104
22AA111 - 190111 - 190
33BB5 - 1045 - 104
44BB111 - 190111 - 190
55CC5 - 1045 - 104
66CC111 - 190111 - 190
77DD5 - 1045 - 104
88DD111 - 190111 - 190

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