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- PDB-2f74: Murine MHC class I H-2Db in complex with human b2-microglobulin a... -

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Basic information

Entry
Database: PDB / ID: 2f74
TitleMurine MHC class I H-2Db in complex with human b2-microglobulin and LCMV-derived immunodminant peptide gp33
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • NONAMERIC PEPTIDE, GP33, DERIVED FROM LYMPHOCYTIC CHORIOMENINGITIS VIRUS
KeywordsIMMUNE SYSTEM / MURINE MHC / LCMV / RECEPTOR BINDING / beta2-microglobulin
Function / homology
Function and homology information


antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class I histocompatibility antigen, D-B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAchour, A. / Michaelsson, J. / Harris, R.A. / Ljunggren, H.G. / Karre, K. / Schneider, G. / Sandalova, T.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structural Basis of the Differential Stability and Receptor Specificity of H-2D(b) in Complex with Murine versus Human beta(2)-Microglobulin.
Authors: Achour, A. / Harris, R.A. / Ljunggren, H.G. / Schneider, G. / Sandalova, T.
#1: Journal: Immunity / Year: 2002
Title: Structural Basis for LCMV Immune Evasion: Subversion of H-2D b and H-2Kb Presentation of gp33 Revealed by Comparative Crystal Structure Analyses.
Authors: Achour, A. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Grufman, P. / Sandberg, J.K. / Levitsky, V. / Kaerre, K. / Sandalova, T. / Schneider, G.
#2: Journal: J.Immunol. / Year: 2004
Title: Determination of structural principles underlying three different modes of lymphocytic choriomeningitis virus escape from CTL recognition.
Authors: Velloso, L.M. / Michaelson, J. / Ljunggren, H.G. / Schneider, G. / Achour, A.
History
DepositionNov 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: NONAMERIC PEPTIDE, GP33, DERIVED FROM LYMPHOCYTIC CHORIOMENINGITIS VIRUS
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: NONAMERIC PEPTIDE, GP33, DERIVED FROM LYMPHOCYTIC CHORIOMENINGITIS VIRUS


Theoretical massNumber of molelcules
Total (without water)90,0256
Polymers90,0256
Non-polymers00
Water1,45981
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: NONAMERIC PEPTIDE, GP33, DERIVED FROM LYMPHOCYTIC CHORIOMENINGITIS VIRUS


Theoretical massNumber of molelcules
Total (without water)45,0123
Polymers45,0123
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-18 kcal/mol
Surface area19460 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: NONAMERIC PEPTIDE, GP33, DERIVED FROM LYMPHOCYTIC CHORIOMENINGITIS VIRUS


Theoretical massNumber of molelcules
Total (without water)45,0123
Polymers45,0123
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-15 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.142, 65.197, 101.941
Angle α, β, γ (deg.)90.00, 102.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31A
41D
51A
61D
71A
81D
91A
101D
111A
121D
131A
141D
151A
161D
171A
181D
191A
201D
211A
221D
231A
241D
12A
22D
32A
42D
52A
62D
72A
82D
92A
102D
112A
122D
132A
142D
152A
162D
13B
23E
33B
43E
53B
63E
73B
83E
93B
103E
113B
123E
133B
143E
153B
163E
173B
183E
193B
203E
14C
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISALAALA1AA3 - 403 - 40
211HISHISALAALA1DD3 - 403 - 40
321GLUGLUTYRTYR5AA41 - 4541 - 45
421GLUGLUTYRTYR5DD41 - 4541 - 45
531GLUGLUGLUGLU2AA46 - 6146 - 61
631GLUGLUGLUGLU2DD46 - 6146 - 61
741ARGARGGLUGLU5AA62 - 6362 - 63
841ARGARGGLUGLU5DD62 - 6362 - 63
951THRTHRSERSER2AA64 - 8864 - 88
1051THRTHRSERSER2DD64 - 8864 - 88
1161ALAALAGLYGLY4AA89 - 9089 - 90
1261ALAALAGLYGLY4DD89 - 9089 - 90
1371GLYGLYTRPTRP2AA91 - 10791 - 107
1471GLYGLYTRPTRP2DD91 - 10791 - 107
1581ARGARGLEULEU5AA108 - 109108 - 109
1681ARGARGLEULEU5DD108 - 109108 - 109
1791LEULEULEULEU2AA110 - 114110 - 114
1891LEULEULEULEU2DD110 - 114110 - 114
19101PHEPHEGLYGLY2AA116 - 120116 - 120
20101PHEPHEGLYGLY2DD116 - 120116 - 120
21111ASPASPARGARG2AA122 - 144122 - 144
22111ASPASPARGARG2DD122 - 144122 - 144
23121ARGARGLYSLYS5AA145 - 146145 - 146
24121ARGARGLYSLYS5DD145 - 146145 - 146
112TRPTRPGLUGLU2AA147 - 154147 - 154
212TRPTRPGLUGLU2DD147 - 154147 - 154
322HISHISLEULEU6AA169 - 179169 - 179
422HISHISLEULEU6DD169 - 179169 - 179
532LEULEUALAALA2AA180 - 187180 - 187
632LEULEUALAALA2DD180 - 187180 - 187
742HISHISGLUGLU5AA192 - 198192 - 198
842HISHISGLUGLU5DD192 - 198192 - 198
952VALVALTHRTHR2AA199 - 225199 - 225
1052VALVALTHRTHR2DD199 - 225199 - 225
1162GLUGLUVALVAL5AA229 - 231229 - 231
1262GLUGLUVALVAL5DD229 - 231229 - 231
1372GLUGLUHISHIS2AA232 - 263232 - 263
1472GLUGLUHISHIS2DD232 - 263232 - 263
1582GLUGLUGLUGLU5AA264 - 275264 - 275
1682GLUGLUGLUGLU5DD264 - 275264 - 275
113THRTHRARGARG2BB4 - 125 - 13
213THRTHRARGARG2EE4 - 125 - 13
323PROPROPHEPHE2BB14 - 3015 - 31
423PROPROPHEPHE2EE14 - 3015 - 31
533GLUGLUVALVAL5BB36 - 3737 - 38
633GLUGLUVALVAL5EE36 - 3737 - 38
743ASPASPGLUGLU2BB38 - 4439 - 45
843ASPASPGLUGLU2EE38 - 4439 - 45
953ARGARGILEILE4BB45 - 4646 - 47
1053ARGARGILEILE4EE45 - 4646 - 47
1163SERSERTHRTHR1BB52 - 7353 - 74
1263SERSERTHRTHR1EE52 - 7353 - 74
1373GLUGLUGLUGLU4BB74 - 7775 - 78
1473GLUGLUGLUGLU4EE74 - 7775 - 78
1583VALVALPROPRO1BB85 - 9086 - 91
1683VALVALPROPRO1EE85 - 9086 - 91
1793LYSLYSILEILE4BB91 - 9292 - 93
1893LYSLYSILEILE4EE91 - 9292 - 93
19103VALVALASPASP2BB93 - 9894 - 99
20103VALVALASPASP2EE93 - 9894 - 99
114LYSLYSMETMET2CC1 - 91 - 9
214LYSLYSMETMET2FF1 - 91 - 9

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H- 2DB


Mass: 32087.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide NONAMERIC PEPTIDE, GP33, DERIVED FROM LYMPHOCYTIC CHORIOMENINGITIS VIRUS


Mass: 1045.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The gp33 PEPTIDE was chemically synthesized.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 8
Details: 20% PEG 6K, pH 8, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0292 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0292 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 22481 / Num. obs: 22481 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 74 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.4 / Num. unique all: 610 / % possible all: 51.4

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7U

1s7u


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.875 / SU B: 19.378 / SU ML: 0.377 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29768 1165 5.2 %RANDOM
Rwork0.22281 ---
all0.22672 ---
obs0.22672 21257 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.548 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å2-0.64 Å2
2--5.39 Å20 Å2
3----3.81 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6338 0 0 81 6419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0216526
X-RAY DIFFRACTIONr_bond_other_d0.0020.025589
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.9328852
X-RAY DIFFRACTIONr_angle_other_deg1.471313022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6755762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027307
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021423
X-RAY DIFFRACTIONr_nbd_refined0.2340.21348
X-RAY DIFFRACTIONr_nbd_other0.2710.26378
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0980.23941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7041.53831
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28126162
X-RAY DIFFRACTIONr_scbond_it1.91832695
X-RAY DIFFRACTIONr_scangle_it3.0424.52690
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1981tight positional0.060.05
2A1129tight positional0.050.05
3B1032tight positional0.060.05
4C137tight positional0.050.05
1A227medium positional10.5
2A353medium positional0.770.5
3B173medium positional0.730.5
2A171loose positional1.15
1A1981tight thermal0.140.5
2A1129tight thermal0.130.5
3B1032tight thermal0.160.5
4C137tight thermal0.240.5
1A227medium thermal0.712
2A353medium thermal0.652
3B173medium thermal0.562
2A171loose thermal1.9410
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.449 54
Rwork0.346 1032
obs-920
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)
15.1343-2.6147-1.74112.99791.32422.218-0.1704-0.2107-0.52320.21740.13360.33740.3158-0.13730.03680.2868-0.1123-0.16010.26870.02180.225717.0310.06511.897
24.3165-2.6478-1.63085.2522.15024.59050.34470.5911-0.2016-0.8699-0.21510.3120.2016-0.2964-0.12960.3375-0.06-0.20640.3406-0.02530.142519.74-2.53-7.725
33.9218-7.85385.937540.01940.02324.347-0.7788-1.6923-0.18751.0551.1341.23960.6476-1.2001-0.35530.2963-0.11630.20110.79460.00370.3336-0.6376.93520.158
45.852-0.6593-1.77841.83560.90564.2814-0.04370.0355-0.32880.01730.1834-0.1650.15490.5848-0.13970.3838-0.1495-0.14930.482-0.11540.21736.34333.5360.357
54.1447-2.1274-3.63612.0641.96848.59190.31140.5159-0.0594-0.55430.0045-0.1815-0.3705-0.1483-0.31590.4118-0.2992-0.02330.7042-0.17310.23398.31933.18240.565
67.1564-5.22461.386821.8869-0.6913.6106-0.4267-2.6444-1.67370.28591.28192.8028-0.127-0.6528-0.85520.2714-0.06680.03530.7039-0.01770.2029-11.76337.12969.808
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1822 - 182
2X-RAY DIFFRACTION1AA183 - 276183 - 276
3X-RAY DIFFRACTION2BB1 - 982 - 99
4X-RAY DIFFRACTION3CC1 - 91 - 9
5X-RAY DIFFRACTION4DD1 - 1821 - 182
6X-RAY DIFFRACTION4DD183 - 276183 - 276
7X-RAY DIFFRACTION5EE1 - 982 - 99
8X-RAY DIFFRACTION6FF1 - 91 - 9

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