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- PDB-3quy: Structure of the mouse CD1d-BnNH-GSL-1'-iNKT TCR complex -

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Basic information

Entry
Database: PDB / ID: 3quy
TitleStructure of the mouse CD1d-BnNH-GSL-1'-iNKT TCR complex
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2 microglobulin
  • Valpha14 (mouse variable domain, human constant domain)
  • Vbeta8.2 (mouse variable domain, human constant domain)
KeywordsIMMUNE SYSTEM / antigen presentation / glycolipid / NKT cells
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of type II interferon production / sensory perception of smell / late endosome / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / lysosome / early endosome / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-QUY / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLi, Y. / Girardi, E. / Yu, E.D. / Zajonc, D.M.
CitationJournal: Embo J. / Year: 2011
Title: Galactose-modified iNKT cell agonists stabilized by an induced fit of CD1d prevent tumour metastasis.
Authors: Aspeslagh, S. / Li, Y. / Yu, E.D. / Pauwels, N. / Trappeniers, M. / Girardi, E. / Decruy, T. / Van Beneden, K. / Venken, K. / Drennan, M. / Leybaert, L. / Wang, J. / Franck, R.W. / Van ...Authors: Aspeslagh, S. / Li, Y. / Yu, E.D. / Pauwels, N. / Trappeniers, M. / Girardi, E. / Decruy, T. / Van Beneden, K. / Venken, K. / Drennan, M. / Leybaert, L. / Wang, J. / Franck, R.W. / Van Calenbergh, S. / Zajonc, D.M. / Elewaut, D.
History
DepositionFeb 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2 microglobulin
C: Valpha14 (mouse variable domain, human constant domain)
D: Vbeta8.2 (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4429
Polymers94,3764
Non-polymers2,0665
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-24 kcal/mol
Surface area36280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.765, 192.005, 150.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 3 types, 3 molecules ABD

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 32632.668 Da / Num. of mol.: 1 / Fragment: UNP residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1.1, CD1d, Cd1d1 / Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P11609
#2: Protein Beta-2 microglobulin


Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: B2m, beta-2-microglobulin, mCG_11606, RP23-34E24.5-001
Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q91XJ8, UniProt: P01887*PLUS
#4: Protein Vbeta8.2 (mouse variable domain, human constant domain)


Mass: 27026.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3

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Antibody , 1 types, 1 molecules C

#3: Antibody Valpha14 (mouse variable domain, human constant domain)


Mass: 23055.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3

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Sugars , 2 types, 3 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: glycosphingolipid
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Details: glycosphingolipid
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 412 molecules

#7: Chemical ChemComp-QUY / (2S,3R,4S,5R,6S)-6-[(2S,3S,4R)-2-(hexacosanoylamino)-3,4-dihydroxy-octadecoxy]-3,4,5-trihydroxy-N-(phenylmethyl)oxane-2-carboxamide


Mass: 961.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C57H104N2O9
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsD219H CONFLICT IN UNP ENTRY P11609

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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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 17% polyethylene glycol 4000, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2010
RadiationMonochromator: side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 53557 / Num. obs: 53289 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2QY7, 3HE6

2qy7

3he6


Resolution: 2.25→35.35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.025 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23073 1112 2 %RANDOM
Rwork0.18952 ---
obs0.19037 53289 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.574 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 140 410 6812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216639
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9519058
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3765813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46424.096293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55315989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2741533
X-RAY DIFFRACTIONr_chiral_restr0.0870.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215081
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.54061
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06726553
X-RAY DIFFRACTIONr_scbond_it1.85332578
X-RAY DIFFRACTIONr_scangle_it2.9534.52505
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 84 -
Rwork0.251 3884 -
obs--99.45 %
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)
11.6055-1.098-0.71192.22051.22063.07150.0030.0097-0.09010.00790.00180.00310.1349-0.0571-0.00480.0194-0.0043-0.02090.03520.01450.043933.670621.0263-17.5611
25.42730.61330.52564.1983-0.0012.4954-0.043-0.7551-0.76810.3621-0.0229-0.78380.10270.29140.06580.14450.0380.02460.22130.12780.471263.9094-0.6444-16.8632
37.9417-0.9387-3.23532.14140.73532.6798-0.0528-0.35730.2923-0.0770.104-0.4746-0.24640.3147-0.05120.1163-0.03840.00560.1258-0.00350.227962.517820.2849-20.3927
44.7553-1.6832.24051.6336-0.73852.0372-0.05670.042-0.05140.00960.03650.07830.0087-0.07580.02020.0673-0.0013-0.00020.0381-0.01480.01276.521939.3443-26.0206
55.19240.79910.68736.9770.69713.6436-0.02360.59160.1266-0.8562-0.1250.4121-0.4742-0.24620.14860.28650.1239-0.0930.3039-0.03730.0797-16.385767.4078-28.6145
61.9977-1.60210.33546.8759-0.49760.8718-0.1103-0.07510.21920.45110.0989-0.0723-0.0633-0.07910.01140.1115-0.0102-0.0160.0695-0.04220.055118.379653.3017-12.12
74.88030.77230.23222.7450.12222.31090.05850.20810.2378-0.131-0.02440.008-0.139-0.0722-0.03420.09660.0542-0.00190.0432-0.00290.0309-6.468370.1517-14.4298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 180
2X-RAY DIFFRACTION1A280
3X-RAY DIFFRACTION1A1 - 5
4X-RAY DIFFRACTION2A181 - 279
5X-RAY DIFFRACTION3B2 - 99
6X-RAY DIFFRACTION4C1 - 112
7X-RAY DIFFRACTION5C113 - 205
8X-RAY DIFFRACTION6D2 - 112
9X-RAY DIFFRACTION7D113 - 240

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