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- PDB-2p82: Cysteine protease ATG4A -

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Basic information

Entry
Database: PDB / ID: 2p82
TitleCysteine protease ATG4A
ComponentsCysteine protease ATG4A
KeywordsHYDROLASE / Autophagy / Protease / Protein transport / Thiol protease / Transport / Ubl conjugation pathway / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Macroautophagy / cysteine-type peptidase activity / autophagy / protein transport / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Autophagin-2 / Peptidase C54 / Peptidase family C54 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Cysteine protease ATG4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Davis, T. / Mujib, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Walker, J.R. / Davis, T. / Mujib, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Citation
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy.
Authors: Marino, G. / Uria, J.A. / Puente, X.S. / Quesada, V. / Bordallo, J. / Lopez-Otin, C.
#2: Journal: J.Cell.Sci. / Year: 2004
Title: LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation.
Authors: Kabeya, Y. / Mizushima, N. / Yamamoto, A. / Oshitani-Okamoto, S. / Ohsumi, Y. / Yoshimori, T.
#3: Journal: J.Biol.Chem. / Year: 2003
Title: The COOH terminus of GATE-16, an intra-Golgi transport modulator, is cleaved by the human cysteine protease HsApg4A.
Authors: Scherz-Shouval, R. / Sagiv, Y. / Shorer, H. / Elazar, Z.
History
DepositionMar 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine protease ATG4A
B: Cysteine protease ATG4A
C: Cysteine protease ATG4A
D: Cysteine protease ATG4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,26020
Polymers162,2944
Non-polymers96616
Water15,457858
1
A: Cysteine protease ATG4A
B: Cysteine protease ATG4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5819
Polymers81,1472
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint7 kcal/mol
Surface area26200 Å2
MethodPISA
2
C: Cysteine protease ATG4A
D: Cysteine protease ATG4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,67911
Polymers81,1472
Non-polymers5329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint16 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.408, 94.408, 337.339
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11D-1-

CL

DetailsTHE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein
Cysteine protease ATG4A / Autophagy-related protein 4 homolog A / hAPG4A / Autophagin-2 / Autophagy-related cysteine ...Autophagy-related protein 4 homolog A / hAPG4A / Autophagin-2 / Autophagy-related cysteine endopeptidase 2 / AUT-like 2 cysteine endopeptidase


Mass: 40573.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG4A, APG4A, AUTL2 / Plasmid: pET28a-LIC-TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8WYN0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 858 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Protein concentration 10 mg/mL. Reservoir: 23.5% PEG3350, 0.2M NaCl, 0.1M SPG buffer pH 5.4, 5% ethylene glycol. Cryoprotected in 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2007
RadiationMonochromator: double crystal and K-B pair of biomorph mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→39 Å / Num. all: 98093 / Num. obs: 98033 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rsym value: 0.063 / Net I/σ(I): 31.86
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 6882 / Rsym value: 0.466 / % possible all: 68.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DLI
Resolution: 2.1→38.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.482 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21279 4967 5.1 %RANDOM
Rwork0.17489 ---
obs0.17679 93002 95.18 %-
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: 39.167 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9891 0 61 858 10810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210284
X-RAY DIFFRACTIONr_angle_refined_deg1.151.95413891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56651245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14224.542469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.946151825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6731548
X-RAY DIFFRACTIONr_chiral_restr0.0790.21484
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027742
X-RAY DIFFRACTIONr_nbd_refined0.1930.24746
X-RAY DIFFRACTIONr_nbtor_refined0.3020.27015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2721
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.237
X-RAY DIFFRACTIONr_mcbond_it0.77726375
X-RAY DIFFRACTIONr_mcangle_it1.31139997
X-RAY DIFFRACTIONr_scbond_it1.73244527
X-RAY DIFFRACTIONr_scangle_it2.50153894
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 255 -
Rwork0.221 4655 -
obs--65.61 %
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)
110.22425.820410.901712.10512.946728.73120.02921.2837-0.7339-1.74961.4202-1.28641.64682.9529-1.44950.09510.06520.07550.1484-0.211-0.025493.752461.6991-4.1278
21.4232-0.3880.36251.71370.01841.841-0.00310.1249-0.1443-0.10660.07950.0261-0.08170.1089-0.07640.00150.0095-0.01050.1887-0.0150.07181.570476.23184.9669
34.166-1.4941-0.23962.9046-0.0146.00280.14620.2785-0.4843-0.25120.05760.32490.2767-0.4866-0.2038-0.0287-0.0265-0.06150.075-0.01790.092171.579964.22534.6634
40.70990.28290.64161.3556-0.13351.4431-0.0307-0.140.0120.20530.0134-0.0917-0.2483-0.11170.01730.02340.0407-0.01110.1249-0.02360.009779.788182.551317.0006
55.5894-2.66783.82061.3999-1.82752.61170.1165-1.1437-0.34710.4802-0.18270.21670.352-0.5470.0662-0.0613-0.00140.03470.2303-0.0310.036375.092672.021423.4081
62.9781-0.1331-2.36314.8033-3.64635.02220.1295-0.35520.14960.4768-0.0521-0.2099-0.43320.2457-0.07740.01260.003-0.020.1058-0.05660.016893.165868.153726.8992
729.6521-0.319-27.00723.9965-2.036526.1797-0.15940.347-1.75090.3206-0.328-0.18281.4981-0.7660.4874-0.0094-0.1172-0.00640.221-0.00720.08575.706258.364835.3795
85.96420.8918-1.08292.68180.59233.05120.22490.03910.15410.1598-0.1028-0.1089-0.29250.187-0.1220.02290.0456-0.04370.1976-0.01620.147793.91770.901117.9183
91.424-0.54460.8570.6338-0.53851.29620.05110.1480.003-0.0719-0.0642-0.0626-0.04790.19840.013-0.01460.01090.00980.1934-0.03170.03186.307375.02723.8857
1032.625614.177716.82999.78962.665922.740.27530.318-0.6346-0.342-0.1525-0.5156-0.49731.0871-0.1228-0.12030.02430.10040.2009-0.0358-0.004598.528175.5436-0.8057
111.7881-0.43360.52610.8186-0.74461.8930.07760.101-0.1248-0.0722-0.0443-0.00680.11760.165-0.0332-0.02460.0268-0.02840.1335-0.030.099196.356362.872117.4601
1273.198357.962753.087773.300262.073153.15121.6425-0.43761.99220.5396-0.1851-0.66580.86930.3045-1.45750.065-0.0523-0.17870.1056-0.1060.163102.720870.257235.8456
1328.95133.5307-3.537814.3481.871616.90580.5468-2.63110.0271.85190.1751-1.5438-1.1851.0494-0.72190.1661-0.1148-0.0490.1842-0.0946-0.043894.473198.631861.2429
146.57330.0268-2.08088.49245.922525.69870.3205-0.71180.8860.7156-0.35360.5365-0.5220.28610.0332-0.0403-0.12670.15110.0469-0.18820.046888.007399.176962.1965
151.51960.94290.0652.23760.9190.90830.1436-0.20510.10520.1062-0.2150.17370.1237-0.19690.07140.0022-0.05590.0310.2115-0.04650.052279.844780.682849.7629
161.0097-0.4918-2.49375.36971.31896.16110.1069-0.94430.8160.6148-0.63021.3743-0.4237-1.01910.5233-0.0480.08730.17670.2369-0.29540.240771.624495.988754.2138
171.26330.2619-0.31722.29010.49211.38870.0887-0.03040.0601-0.2109-0.1290.10440.0206-0.20320.0403-0.006-0.0162-0.00530.1606-0.04040.019580.07377.802740.1697
185.28351.5737-0.47012.1829-0.36562.9854-0.16980.3462-0.2327-0.25250.06220.1514-0.2351-0.04810.10760.11320.0034-0.02930.0914-0.06870.017687.304190.936231.9119
1914.978-5.623315.95124.7254-3.386727.1568-0.290500.9667-0.2016-0.3591-0.046-2.2903-1.36110.64960.12850.1758-0.10730.06620.0014-0.005979.159199.805725.6145
204.3245-0.07580.95142.44230.01972.50720.0206-0.1238-0.36420.05970.0357-0.1468-0.10860.5322-0.0563-0.0229-0.05420.03920.2091-0.0107-0.0008100.89487.495144.4573
211.44381.0078-0.19771.36760.0331.95850.1294-0.3090.02340.0922-0.22010.0692-0.0331-0.06250.09070.0155-0.03780.0360.2107-0.0670.038485.136884.46552.9707
220.71070.6116-0.27740.74880.55072.90990.026-0.12270.080.0037-0.02950.0343-0.22950.16840.00350.0379-0.04770.02130.1164-0.04140.059290.643991.473648.0795
233.03990.64340.64722.0193-0.75852.0299-0.1557-0.02940.2447-0.30690.16540.105-0.19040.3096-0.00980.0543-0.14320.04930.1516-0.0387-0.0299102.998598.319839.3264
2465.0134-32.0403-17.595927.704811.02165.22582.32512.7142-2.0796-0.7991-3.3045-3.2196-0.70980.41610.97940.4099-0.0004-0.00290.4175-0.00380.4138102.220290.100821.0284
2512.1353-3.8965-1.332813.43645.55367.62420.81310.44391.447-0.8793-0.58870.4969-1.6248-0.4083-0.22440.20580.08510.071-0.03180.0120.092131.1469116.263321.8026
261.02570.2877-0.47451.60630.62821.98790.0846-0.08610.1333-0.0794-0.06590.09-0.32570.0682-0.01870.09450.0170.0210.0730.0140.06741.3588101.068513.1706
276.1892-0.2174-1.04275.8030.1334.7581-0.1063-0.40160.5079-0.03910.3417-0.8382-0.83570.6665-0.23540.0909-0.15370.05290.1048-0.12170.057850.7778107.990123.8971
280.90360.7457-0.02531.64950.44231.74530.0407-0.1263-0.08260.0481-0.0726-0.09150.06380.11430.0320.02640.01110.00010.0760.00970.01642.83388.36417.1881
2920.4351.913-5.10343.78360.39851.48750.3217-0.7191-1.42710.3847-0.3392-0.7179-0.35610.23560.0175-0.0367-0.048-0.04490.15320.06870.095648.094690.876328.5771
308.86550.42414.17661.82811.13813.52510.4279-0.3206-0.69730.1341-0.21710.30660.3639-0.4859-0.21080.0532-0.07370.00330.06330.01730.050328.780189.895834.4095
318.67722.2801-0.020813.86693.66821.01720.7277-1.4248-0.65131.3197-0.4731-1.61650.18050.7879-0.2546-0.0276-0.1034-0.15510.45260.17150.004443.865589.804643.7334
3213.65361.16477.14992.72520.44997.69680.17440.01720.1094-0.0104-0.11790.1650.1464-0.2246-0.05650.1006-0.00590.03180.1282-0.02580.08428.762494.9326.6177
331.3086-0.3693-0.73631.25630.35142.18450.1107-0.05520.0795-0.0725-0.05560.0609-0.2462-0.0681-0.05510.07940.01960.00430.055-0.00910.062833.7899102.524416.0222
343.8333-0.3977-0.26180.6147-0.051.3110.07880.08660.3458-0.044-0.0236-0.0362-0.3049-0.0528-0.05520.12820.00940.03120.0413-0.00130.055136.4989105.28810.9521
352.18830.4148-0.29472.1936-0.13651.35040.157-0.28210.15960.1625-0.1180.2422-0.1601-0.0598-0.0390.0547-0.03560.0510.1213-0.04510.030127.7236100.339934.8853
36188.3343158.170118.3304187.463741.615114.3699-1.16132.97018.8877-4.6451-0.23038.9595-1.89950.41791.39160.3014-0.0562-0.03260.4007-0.02810.333221.308679.909239.2266
3710.9615-5.81371.268218.4017-8.05519.04040.319-0.2495-1.7078-0.01090.14630.70350.6877-0.2827-0.4653-0.0466-0.0081-0.0942-0.07320.04680.217734.843943.333233.0088
382.56970.9071.28372.3550.99082.19010.1713-0.1852-0.18420.214-0.1371-0.33990.04060.177-0.03420.0096-0.0599-0.08330.14470.13160.093546.544764.440742.9111
392.5154-0.214-0.78161.56931.06824.35240.11140.1854-0.406-0.0632-0.0618-0.42080.31920.341-0.0496-0.05380.0081-0.03310.08710.05160.149647.700558.846430.0345
401.5466-0.27230.29241.95460.25521.47610.1143-0.09080.01290.0175-0.1867-0.2111-0.22060.14580.0724-0.0068-0.0674-0.04690.10480.06410.053244.537974.146935.0558
4125.5087-0.38032.72080.0057-0.04060.2902-0.18980.64240.1254-0.7089-0.0782-0.5366-0.2509-0.23620.2681-0.04210.00790.09090.14680.06690.137748.880471.133722.6505
426.01210.37420.69773.2952-1.41272.40610.1967-0.43720.35860.04550.02190.3117-0.3771-0.1947-0.21850.0303-0.0148-0.00920.07380.02360.054127.952171.755722.6921
4314.06513.3146-3.690217.9955-6.13788.4325-0.0740.93080.1834-0.6608-0.1906-0.0203-0.55470.48480.26460.0774-0.0516-0.00950.10010.0622-0.041534.889471.488812.6101
447.4397-0.0689-4.01663.42870.57545.620.22540.05910.1438-0.047-0.0496-0.0509-0.3184-0.0008-0.17580.07040.0192-0.05570.12690.02420.110130.908867.459326.2388
452.43510.78260.84531.2198-0.02461.28230.1799-0.1749-0.21660.1179-0.1154-0.17760.0810.0732-0.06450.0087-0.0318-0.05060.1060.07960.078338.331759.09437.7344
4612.0097-4.3233-1.17363.691-0.39310.742-0.0219-0.201-0.56340.5716-0.0566-0.34560.13040.05540.07850.0267-0.0812-0.10050.06940.09090.063432.055854.715443.5574
471.40490.4913-0.23541.387-0.75241.9013-0.03890.1352-0.0704-0.19120.05260.02110.09690.0321-0.01380.0324-0.0155-0.03580.08690.00970.059627.163360.786921.3331
4862.3032-12.98113.47132.7046-2.80682.9128-0.5548-0.21445.81810.9680.7023-2.2079-1.87380.9637-0.14750.31140.0004-0.00740.3348-0.00490.314623.46674.554213.1905
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 3122 - 27
2X-RAY DIFFRACTION2AA32 - 9328 - 89
3X-RAY DIFFRACTION3AA94 - 11090 - 106
4X-RAY DIFFRACTION4AA111 - 159107 - 155
5X-RAY DIFFRACTION5AA160 - 168156 - 164
6X-RAY DIFFRACTION6AA169 - 186165 - 182
7X-RAY DIFFRACTION7AA187 - 216183 - 212
8X-RAY DIFFRACTION8AA217 - 237213 - 233
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22X-RAY DIFFRACTION22BB300 - 334296 - 330
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24X-RAY DIFFRACTION24BB354 - 359350 - 355
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29X-RAY DIFFRACTION29CC161 - 169157 - 165
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31X-RAY DIFFRACTION31CC183 - 192179 - 188
32X-RAY DIFFRACTION32CC218 - 237214 - 233
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34X-RAY DIFFRACTION34CC294 - 317290 - 313
35X-RAY DIFFRACTION35CC318 - 354314 - 350
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