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- PDB-3iwu: Crystal structure of Y116T/I16A double mutant of 5-hydroxyisourat... -

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Basic information

Entry
Database: PDB / ID: 3iwu
TitleCrystal structure of Y116T/I16A double mutant of 5-hydroxyisourate hydrolase
Components5-hydroxyisourate hydrolase
KeywordsHYDROLASE / HIUase / Transthyretin / TRP / thyroid hormones / molecular evolution / Peroxisome / Purine metabolism
Function / homology
Function and homology information


hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / urate catabolic process / purine nucleobase metabolic process / peroxisome
Similarity search - Function
Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like ...Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-hydroxyisourate hydrolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCendron, L. / Ramazzina, I. / Berni, R. / Percudani, R. / Zanotti, G.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Probing the evolution of hydroxyisourate hydrolase into transthyretin through active-site redesign.
Authors: Cendron, L. / Ramazzina, I. / Percudani, R. / Rasore, C. / Zanotti, G. / Berni, R.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Structure of zebra fish HIUase: insights into evolution of an enzyme to a hormone transporter
Authors: Zanotti, G. / Cendron, L. / Ramazzina, I. / Folli, C. / Percudani, R. / Berni, R.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-hydroxyisourate hydrolase
B: 5-hydroxyisourate hydrolase
C: 5-hydroxyisourate hydrolase
D: 5-hydroxyisourate hydrolase
E: 5-hydroxyisourate hydrolase
F: 5-hydroxyisourate hydrolase
G: 5-hydroxyisourate hydrolase
H: 5-hydroxyisourate hydrolase


Theoretical massNumber of molelcules
Total (without water)123,1978
Polymers123,1978
Non-polymers00
Water11,458636
1
A: 5-hydroxyisourate hydrolase
B: 5-hydroxyisourate hydrolase
C: 5-hydroxyisourate hydrolase
D: 5-hydroxyisourate hydrolase


Theoretical massNumber of molelcules
Total (without water)61,5984
Polymers61,5984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-40 kcal/mol
Surface area19240 Å2
MethodPISA
2
E: 5-hydroxyisourate hydrolase
F: 5-hydroxyisourate hydrolase
G: 5-hydroxyisourate hydrolase
H: 5-hydroxyisourate hydrolase


Theoretical massNumber of molelcules
Total (without water)61,5984
Polymers61,5984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-41 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.580, 66.592, 236.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASPAA7 - 3326 - 52
21SERSERASPASPBB7 - 3326 - 52
31SERSERASPASPCC7 - 3326 - 52
41SERSERASPASPDD7 - 3326 - 52
51SERSERASPASPEE7 - 3326 - 52
61SERSERASPASPFF7 - 3326 - 52
71SERSERASPASPGG7 - 3326 - 52
81SERSERASPASPHH7 - 3326 - 52
12THRTHRPROPROAA44 - 5463 - 73
22THRTHRPROPROBB44 - 5463 - 73
32THRTHRPROPROCC44 - 5463 - 73
42THRTHRPROPRODD44 - 5463 - 73
52THRTHRPROPROEE44 - 5463 - 73
62THRTHRPROPROFF44 - 5463 - 73
72THRTHRPROPROGG44 - 5463 - 73
82THRTHRPROPROHH44 - 5463 - 73
13PHEPHETHRTHRAA62 - 11581 - 134
23PHEPHETHRTHRBB62 - 11581 - 134
33PHEPHETHRTHRCC62 - 11581 - 134
43PHEPHETHRTHRDD62 - 11581 - 134
53PHEPHETHRTHREE62 - 11581 - 134
63PHEPHETHRTHRFF62 - 11581 - 134
73PHEPHETHRTHRGG62 - 11581 - 134
83PHEPHETHRTHRHH62 - 11581 - 134

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Components

#1: Protein
5-hydroxyisourate hydrolase / HIU hydrolase / HIUHase / Transthyretin-related protein


Mass: 15399.574 Da / Num. of mol.: 8 / Mutation: Y116T, I16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: urah / Plasmid: pET28b-HIUase / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06S87, hydroxyisourate hydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES, 20% PEG10,000, pH7.5, VAPOR DIFFUSION, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.983 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 2.3→66.52 Å / Num. all: 46362 / Num. obs: 46362 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 6 / Num. unique all: 6632 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H1X
Resolution: 2.3→66.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 12.52 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24283 2348 5.1 %RANDOM
Rwork0.17711 ---
all0.18035 46362 --
obs0.18035 44005 99.77 %-
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: 21.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→66.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7144 0 0 636 7780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0227336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.94510024
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04822.895304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.574151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.4461540
X-RAY DIFFRACTIONr_chiral_restr0.1160.21152
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215568
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_it0.9321.54536
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80827392
X-RAY DIFFRACTIONr_scbond_it3.09232800
X-RAY DIFFRACTIONr_scangle_it4.8844.52632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A368medium positional0.130.5
B368medium positional0.150.5
C368medium positional0.130.5
D368medium positional0.10.5
E368medium positional0.150.5
F368medium positional0.150.5
G368medium positional0.110.5
H368medium positional0.120.5
A359loose positional0.315
B359loose positional0.45
C359loose positional0.35
D359loose positional0.265
E359loose positional0.325
F359loose positional0.415
G359loose positional0.315
H359loose positional0.335
A368medium thermal1.112
B368medium thermal1.282
C368medium thermal0.972
D368medium thermal0.932
E368medium thermal1.222
F368medium thermal0.92
G368medium thermal1.172
H368medium thermal0.962
A359loose thermal1.3810
B359loose thermal1.510
C359loose thermal1.2710
D359loose thermal1.1410
E359loose thermal1.410
F359loose thermal1.3110
G359loose thermal1.3910
H359loose thermal1.4310
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 163 -
Rwork0.179 3169 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.67870.5399-0.34941.9447-0.43170.931-0.01230.05650.0475-0.09550.0091-0.0553-0.04010.03940.00320.02870.02380.00340.0475-0.00870.03327.0679-0.3691-63.4296
24.64441.47650.17166.03520.08673.52980.01290.31490.0848-0.18030.0499-0.40980.01650.4216-0.06290.05690.00980.00590.07010.00140.038430.801210.3051-66.6609
31.29810.2927-0.30031.3968-0.21880.90210.0127-0.0149-0.0525-0.02320.0084-0.11770.0149-0.0011-0.02110.02370.0040.00440.05270.00780.040720.2288-0.5264-62.1918
41.08671.1331-0.05173.05891.21253.24920.1203-0.1702-0.07650.0221-0.1605-0.2839-0.02410.08120.04020.04180.01060.00440.06640.00910.094716.143-0.5797-55.7328
50.9949-0.4104-0.14670.77390.65051.7216-0.0008-0.00070.0038-0.0407-0.0503-0.0102-0.011-0.18260.05110.04220.01170.00240.04570.00570.00963.19097.6324-66.645
62.02020.0823-0.09385.16453.12513.95390.05690.0482-0.009-0.2567-0.2620.3732-0.2063-0.57850.2050.01790.0167-0.02120.1226-0.00610.0305-2.29683.1603-68.067
71.48670.71090.13871.99140.27661.6726-0.03430.01280.0251-0.05230.03060.06270.0044-0.07620.00370.03180.0181-0.00310.06310.01290.0258.02947.5081-62.6395
80.7623-0.2968-0.18333.32370.08952.6211-0.0469-0.1262-0.0001-0.0334-0.12810.29470.0797-0.21920.1750.04870.0302-0.00410.0939-0.01380.058910.5185.7523-56.0237
91.7003-0.399-0.32912.07841.49462.78880.0182-0.14930.06640.148-0.05440.0668-0.1085-0.1420.03630.0603-0.02630.00240.06850.00010.0152-2.8505-0.6016-38.1729
107.4564-3.34520.90333.95550.43827.19110.1868-0.44280.05520.3873-0.1710.706-0.1841-0.646-0.01580.1324-0.05790.14470.1135-0.09330.2373-4.20369.4717-32.4171
111.56410.40010.07781.27340.20591.09120.0016-0.03820.0650.1141-0.03670.0196-0.0295-0.06450.0350.0555-0.0175-0.00140.0953-0.00650.00383.9299-1.9519-39.558
122.7748-0.2197-0.87864.45710.15772.75550.0313-0.0224-0.0445-0.2636-0.09150.524-0.2102-0.06180.06020.0444-0.009-0.02690.0912-0.00970.06858.2017-1.1705-45.8268
131.2302-0.00710.76583.5355-1.30791.66170.02170.0353-0.04540.1353-0.0243-0.07620.0827-0.01350.00260.0413-0.0207-0.01350.0644-0.01410.019523.1132.8705-37.2995
141.536-0.6441-0.23472.8621-0.83324.52350.1411-0.1756-0.07620.206-0.09410.0070.20060.0509-0.04690.08-0.0396-0.0380.07290.00840.040424.6105-1.5196-30.6535
1510.0093-4.851-1.30525.2428-2.48884.16520.169-0.4975-0.16190.0671-0.2384-0.5372-0.08530.34870.06950.0633-0.0751-0.16570.11950.22720.604822.6691-9.7307-30.3131
161.351-0.47370.35672.5644-0.7191.25920.0298-0.0128-0.06050.0831-0.0232-0.13360.04010.0433-0.00660.0472-0.0214-0.00780.0714-0.00040.044416.93053.0722-38.8599
171.7557-0.81390.36172.2188-1.19921.8758-0.0261-0.1161-0.09610.15730.0033-0.0389-0.09220.04830.02290.0503-0.0236-0.00970.0823-0.0220.027726.6522-1.3814-90.7905
182.6802-0.53380.83842.3772-0.15541.48380.0319-0.2316-0.2670.1859-0.0573-0.1457-0.09630.34890.02540.0555-0.0287-0.03880.18340.06270.056629.5282-8.4193-89.9218
193.2888-0.1146-0.83892.07851.09711.02960.02030.05260.21760.08840.0795-0.1054-0.22370.1065-0.09990.2701-0.0577-0.01620.0541-0.00280.020622.342210.7079-94.9421
201.2964-0.1256-0.27462.052-0.74041.8546-0.0016-0.0004-0.11820.05370.0031-0.14580.1010.1322-0.00150.0510.0081-0.02120.0502-0.0080.034221.6095-5.0677-97.4346
211.3051-0.6015-0.56412.08111.10721.83540.0527-0.01960.05980.0794-0.0423-0.0065-0.1616-0.1352-0.01030.05890.00280.01610.09430.02660.02934.00313.0476-96.312
221.28970.38110.80220.92081.17441.67070.1252-0.01720.08-0.0682-0.23070.0908-0.1011-0.37870.10550.09470.08020.02410.17240.01580.02471.01157.5753-92.9264
231.1035-0.15610.29321.7946-0.26681.47030.0126-0.02730.03480.08740.03590.1388-0.076-0.1048-0.04850.07340.01450.0220.0888-0.00270.01728.06390.2998-96.8858
243.9295-1.5505-0.45139.29641.26272.76530.0160.15510.1221-0.21240.00840.0036-0.2017-0.1722-0.02440.0845-0.00890.0240.0873-0.00920.013712.1861-1.0331-102.8788
251.8790.31880.58951.10060.72682.2123-0.08030.07280.0925-0.0543-0.0280.1256-0.0726-0.12970.10830.08960.0150.00230.0340.02090.04298.61666.0609-124.2027
267.3623-1.1272-0.75495.21280.58973.3333-0.0250.20610.0892-0.38880.01220.3604-0.2306-0.26670.01280.08780.0062-0.02550.0470.01320.03132.6997-2.1498-129.0345
271.51120.28470.23580.84120.1651.268-0.01540.02740.0504-0.06810.03530.0127-0.15710.0348-0.01990.08780.0180.00390.04390.00720.026914.17934.3486-121.0692
284.03063.34350.73775.20520.213.78260.0902-0.188-0.00680.2037-0.0590.1007-0.063-0.1816-0.03110.11370.0381-0.01390.03370.00880.032315.90293.3556-113.7423
291.59860.5137-0.6281.1794-0.63111.3998-0.0522-0.0004-0.0006-0.1105-0.0086-0.1554-0.05560.13740.06090.0613-0.00810.02340.02630.00470.026630.4316-8.3953-119.7108
3010.38610.5850.36924.4952-0.74164.45550.1650.0605-0.26510.0713-0.2335-0.677-0.05740.49160.06850.0533-0.0186-0.01050.0620.02940.105436.89820.3756-124.1521
311.5277-0.36860.09911.08860.03571.5454-0.00380.0312-0.0269-0.01650.038-0.062-0.06670.0245-0.03430.07780.01820.00630.05020.01370.012823.7024-6.4008-118.7206
324.75532.0203-0.52564.7270.91852.802-0.0289-0.31050.07090.043-0.0071-0.1876-0.07310.27110.0360.09610.03160.01160.05670.01050.038419.7335-4.3568-112.5805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 58
2X-RAY DIFFRACTION2A59 - 69
3X-RAY DIFFRACTION3A70 - 106
4X-RAY DIFFRACTION4A107 - 119
5X-RAY DIFFRACTION5B6 - 48
6X-RAY DIFFRACTION6B49 - 69
7X-RAY DIFFRACTION7B70 - 107
8X-RAY DIFFRACTION8B108 - 119
9X-RAY DIFFRACTION9C6 - 58
10X-RAY DIFFRACTION10C59 - 69
11X-RAY DIFFRACTION11C70 - 106
12X-RAY DIFFRACTION12C107 - 119
13X-RAY DIFFRACTION13D6 - 33
14X-RAY DIFFRACTION14D34 - 59
15X-RAY DIFFRACTION15D60 - 69
16X-RAY DIFFRACTION16D70 - 119
17X-RAY DIFFRACTION17E6 - 48
18X-RAY DIFFRACTION18E49 - 68
19X-RAY DIFFRACTION19E69 - 88
20X-RAY DIFFRACTION20E89 - 119
21X-RAY DIFFRACTION21F6 - 37
22X-RAY DIFFRACTION22F38 - 70
23X-RAY DIFFRACTION23F71 - 106
24X-RAY DIFFRACTION24F107 - 119
25X-RAY DIFFRACTION25G6 - 55
26X-RAY DIFFRACTION26G56 - 69
27X-RAY DIFFRACTION27G70 - 106
28X-RAY DIFFRACTION28G107 - 119
29X-RAY DIFFRACTION29H6 - 58
30X-RAY DIFFRACTION30H59 - 69
31X-RAY DIFFRACTION31H70 - 106
32X-RAY DIFFRACTION32H107 - 119

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