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- PDB-6u7f: HCoV-229E RBD Class IV in complex with human APN -

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Basic information

Entry
Database: PDB / ID: 6u7f
TitleHCoV-229E RBD Class IV in complex with human APN
Components
  • Aminopeptidase N
  • Spike glycoprotein
KeywordsHYDROLASE/VIRAL PROTEIN / CoV / coronavirus / 229E / spike glycoprotein / APN / S-protein / HYDROLASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / host cell membrane / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding ...alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / host cell membrane / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding / secretory granule membrane / metallopeptidase activity / signaling receptor activity / virus receptor activity / angiogenesis / cell differentiation / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion membrane / proteolysis / extracellular space / extracellular exosome / zinc ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain ...Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Aminopeptidase N / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsTomlinson, A.C.A. / Li, Z. / Rini, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Elife / Year: 2019
Title: The human coronavirus HCoV-229E S-protein structure and receptor binding.
Authors: Zhijie Li / Aidan Ca Tomlinson / Alan Hm Wong / Dongxia Zhou / Marc Desforges / Pierre J Talbot / Samir Benlekbir / John L Rubinstein / James M Rini /
Abstract: The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S- ...The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S-protein function is maintained is not understood. Reported are the X-ray crystal structures of Class III-V RBDs in complex with human aminopeptidase N (hAPN), as well as the electron cryomicroscopy structure of the 229E S-protein. The structures show that common core interactions define the specificity for hAPN and that the peripheral RBD sequence variation is accommodated by loop plasticity. The results provide insight into immune evasion and the cross-species transmission of 229E and related coronaviruses. We also find that the 229E S-protein can expose a portion of its helical core to solvent. This is undoubtedly facilitated by hydrophilic subunit interfaces that we show are conserved among coronaviruses. These interfaces likely play a role in the S-protein conformational changes associated with membrane fusion.
History
DepositionSep 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 6, 2020Group: Data collection / Database references / Category: chem_comp / pdbx_related_exp_data_set / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase N
B: Aminopeptidase N
C: Spike glycoprotein
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,66925
Polymers238,5224
Non-polymers5,14721
Water4,107228
1
A: Aminopeptidase N
C: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,94513
Polymers119,2612
Non-polymers2,68411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase N
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,72412
Polymers119,2612
Non-polymers2,46310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.158, 98.572, 147.778
Angle α, β, γ (deg.)90.000, 104.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 66 through 967 or resid 5001 through 5010))
21chain B
12(chain C and (resid 302 through 340 or resid 348 through 415 or resid 2001 through 2002))
22(chain D and (resid 302 through 371 or resid 385 through 415 or resid 2001 through 2002))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPLYSLYS(chain A and (resid 66 through 967 or resid 5001 through 5010))AA66 - 9675 - 906
121ZNZNNAGNAG(chain A and (resid 66 through 967 or resid 5001 through 5010))AI - N5001 - 5010
211ASPASPLYSLYSchain BBB66 - 9675 - 906
112ILEILECYSCYS(chain C and (resid 302 through 340 or resid 348 through 415 or resid 2001 through 2002))CC302 - 34014 - 52
122THRTHRVALVAL(chain C and (resid 302 through 340 or resid 348 through 415 or resid 2001 through 2002))CC348 - 41560 - 127
132NAGNAGNAGNAG(chain C and (resid 302 through 340 or resid 348 through 415 or resid 2001 through 2002))CV - W2001 - 2002
212ILEILEPHEPHE(chain D and (resid 302 through 371 or resid 385 through 415 or resid 2001 through 2002))DD302 - 37114 - 83
222PHEPHEVALVAL(chain D and (resid 302 through 371 or resid 385 through 415 or resid 2001 through 2002))DD385 - 41597 - 127
232NAGNAGNAGNAG(chain D and (resid 302 through 371 or resid 385 through 415 or resid 2001 through 2002))DX - Y2001 - 2002

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Aminopeptidase N / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma ...hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma membrane glycoprotein CD13 / gp150


Mass: 103522.031 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 66-967)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANPEP, APN, CD13, PEPN / Plasmid: PB-T-PAF / Cell line (production host): HEK293S GnT1-minus / Production host: Homo sapiens (human) / References: UniProt: P15144, membrane alanyl aminopeptidase
#2: Protein Spike glycoprotein


Mass: 15739.073 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Plasmid: PB-T-PAF / Cell line (production host): HEK293S GnT1-minus / Production host: Homo sapiens (human) / References: UniProt: Q1HVL3*PLUS

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Sugars , 2 types, 19 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 15
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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 , 2 types, 230 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 21, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.75→49.382 Å / Num. obs: 72016 / % possible obs: 99.8 % / Redundancy: 3.794 % / Biso Wilson estimate: 51.113 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.079 / Χ2: 0.981 / Net I/σ(I): 16.24 / Num. measured all: 273221
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.75-2.823.8460.4483.5120339528952880.9010.521100
2.82-2.893.8450.3674.3219896518551740.9290.42799.8
2.89-2.983.8390.3274.8819272502950200.9380.3899.8
2.98-3.073.8340.2496.2718702488648780.9630.28999.8
3.07-3.173.8180.1967.7318134475047490.9720.228100
3.17-3.283.8110.1519.6417450458245790.9820.17699.9
3.28-3.43.8070.11711.716901445244390.9890.13799.7
3.4-3.543.7850.0914.4615997422542260.9920.105100
3.54-3.73.7850.07416.9915442409240800.9940.08699.7
3.7-3.883.7720.05919.9914784392739190.9960.06999.8
3.88-4.093.7560.05322.2814019373437320.9970.06199.9
4.09-4.343.7430.04525.0513180353335210.9970.05399.7
4.34-4.643.7520.03928.0712411331033080.9980.04699.9
4.64-5.013.7630.03729.0411610309330850.9980.04499.7
5.01-5.493.7630.03728.910739285628540.9980.04499.9
5.49-6.143.7850.0427.829819260025940.9970.04699.8
6.14-7.093.7740.03529.178615228822830.9980.04199.8
7.09-8.683.7720.02834.037276193019290.9980.03399.9
8.68-12.283.7170.02538.415643152415180.9990.02999.6
12.28-49.3823.5620.02438.9729928588400.9980.02897.9

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Processing

Software
NameVersionClassification
PHENIX1.16rc1_3535refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FYQ

4fyq


Resolution: 2.75→49.382 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 3591 5 %
Rwork0.1904 68199 -
obs0.1922 71790 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.94 Å2 / Biso mean: 53.0345 Å2 / Biso min: 19.13 Å2
Refinement stepCycle: final / Resolution: 2.75→49.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16023 0 324 228 16575
Biso mean--76.06 44.04 -
Num. residues----1993
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8642X-RAY DIFFRACTION9.624TORSIONAL
12B8642X-RAY DIFFRACTION9.624TORSIONAL
21C812X-RAY DIFFRACTION9.624TORSIONAL
22D812X-RAY DIFFRACTION9.624TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.78620.27471370.26732598100
2.7862-2.82440.28891400.25252641100
2.8244-2.86470.29061350.25252582100
2.8647-2.90750.29741380.26742608100
2.9075-2.95290.33241380.27222593100
2.9529-3.00130.30121370.25422608100
3.0013-3.0530.30261360.23972583100
3.053-3.10850.26891410.23852665100
3.1085-3.16830.26681360.22632601100
3.1683-3.2330.25751370.22762583100
3.233-3.30330.27981380.22532641100
3.3033-3.38010.27341350.22842583100
3.3801-3.46460.22311390.21632632100
3.4646-3.55820.2551380.21372646100
3.5582-3.66290.24021390.19872611100
3.6629-3.78110.2241370.18472602100
3.7811-3.91620.22941370.18532611100
3.9162-4.07290.20141360.17432607100
4.0729-4.25820.20851400.16252641100
4.2582-4.48250.18291380.15342643100
4.4825-4.76320.17261380.14042608100
4.7632-5.13060.17561390.14662656100
5.1306-5.64620.18581390.16042628100
5.6462-6.46170.21621390.17872637100
6.4617-8.13520.18351390.17582675100
8.1352-49.3820.20991450.1689271699
Refinement TLS params.Method: refined / Origin x: -25.2671 Å / Origin y: -23.7659 Å / Origin z: -35.7984 Å
111213212223313233
T0.2615 Å2-0.0192 Å20.005 Å2-0.2149 Å20.0263 Å2--0.2234 Å2
L0.5801 °2-0.1538 °2-0.0155 °2-0.1761 °2-0.0153 °2--0.3284 °2
S-0.0215 Å °-0.0842 Å °-0.0737 Å °0.0031 Å °0.0526 Å °0.0197 Å °-0.0044 Å °0.001 Å °-0.0328 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA66 - 967
2X-RAY DIFFRACTION1allA5001 - 5011
3X-RAY DIFFRACTION1allB66 - 967
4X-RAY DIFFRACTION1allB5001 - 5011
5X-RAY DIFFRACTION1allC302 - 415
6X-RAY DIFFRACTION1allC2001 - 2002
7X-RAY DIFFRACTION1allD302 - 417
8X-RAY DIFFRACTION1allD2001 - 2002
9X-RAY DIFFRACTION1allS1 - 228

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