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- PDB-5mgy: Crystal structure of Pseudomonas stutzeri flavinyl transferase Ap... -

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Basic information

Entry
Database: PDB / ID: 5mgy
TitleCrystal structure of Pseudomonas stutzeri flavinyl transferase ApbE, apo form
ComponentsFAD:protein FMN transferase
KeywordsPROTEIN BINDING / FAD binding protein flavinyl transferase
Function / homology
Function and homology information


protein flavinylation / FAD:protein FMN transferase / transferase activity / metal ion binding / plasma membrane
Similarity search - Function
: / T-fold / ApbE-like domains / Flavin transferase ApbE / ApbE family / ApbE-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
FAD:protein FMN transferase
Similarity search - Component
Biological speciesPseudomonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsZhang, L. / Trncik, C. / Andrade, S.L.A. / Einsle, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council310656 Germany
CitationJournal: Biochim. Biophys. Acta / Year: 2016
Title: The flavinyl transferase ApbE of Pseudomonas stutzeri matures the NosR protein required for nitrous oxide reduction.
Authors: Zhang, L. / Trncik, C. / Andrade, S.L. / Einsle, O.
History
DepositionNov 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / reflns_shell / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene ..._entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: FAD:protein FMN transferase
B: FAD:protein FMN transferase
G: FAD:protein FMN transferase
A: FAD:protein FMN transferase
C: FAD:protein FMN transferase
D: FAD:protein FMN transferase
E: FAD:protein FMN transferase
F: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,33316
Polymers288,1388
Non-polymers1948
Water81145
1
H: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers36,0171
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers36,0171
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers36,0171
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers36,0171
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers36,0171
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers36,0171
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
E: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers36,0171
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
F: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers36,0171
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.656, 91.983, 138.061
Angle α, β, γ (deg.)90.00, 90.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21B
12H
22G
13H
23A
14H
24C
15H
25D
16H
26E
17H
27F
18B
28G
19B
29A
110B
210C
111B
211D
112B
212E
113B
213F
114G
214A
115G
215C
116G
216D
117G
217E
118G
218F
119A
219C
120A
220D
121A
221E
122A
222F
123C
223D
124C
224E
125C
225F
126D
226E
127D
227F
128E
228F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111H29 - 348
2111B29 - 348
1121H29 - 345
2121G29 - 345
1131H29 - 348
2131A29 - 348
1141H29 - 348
2141C29 - 348
1151H29 - 348
2151D29 - 348
1161H29 - 348
2161E29 - 348
1171H29 - 348
2171F29 - 348
1181B29 - 345
2181G29 - 345
1191B29 - 348
2191A29 - 348
11101B29 - 348
21101C29 - 348
11111B29 - 348
21111D29 - 348
11121B29 - 348
21121E29 - 348
11131B29 - 348
21131F29 - 348
11141G29 - 345
21141A29 - 345
11151G29 - 345
21151C29 - 345
11161G29 - 345
21161D29 - 345
11171G29 - 345
21171E29 - 345
11181G29 - 345
21181F29 - 345
11191A29 - 348
21191C29 - 348
11201A29 - 348
21201D29 - 348
11211A29 - 348
21211E29 - 348
11221A29 - 348
21221F29 - 348
11231C29 - 348
21231D29 - 348
11241C29 - 348
21241E29 - 348
11251C29 - 348
21251F29 - 348
11261D29 - 348
21261E29 - 348
11271D29 - 348
21271F29 - 348
11281E29 - 348
21281F29 - 348

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.443661, 0.035364, 0.895497), (-0.037632, 0.999075, -0.02081), (-0.895404, -0.024466, 0.444581)-89.75872, 13.41462, 165.656021
3given(1), (1), (1)
4given(-0.999157, -0.040653, 0.005729), (-0.040575, 0.99909, 0.013141), (-0.006258, 0.012897, -0.999897)-0.74542, -3.18193, 270.516785
5given(1), (1), (1)
6given(-0.444757, 0.038495, -0.894824), (0.03459, 0.999069, 0.025788), (0.894983, -0.019483, -0.445674)89.706291, 5.52171, 102.415527
7given(1), (1), (1)
8given(-0.897057, 0.058773, 0.437988), (0.061168, 0.99809, -0.008652), (-0.43766, 0.01903, -0.898939)32.5023, 6.52345, 224.284424
9given(1), (1), (1)
10given(0.893188, 0.058297, -0.445888), (-0.06659, 0.997776, -0.002938), (0.444725, 0.032316, 0.895084)-31.13928, 14.75033, 44.712139
11given(1), (1), (1)
12given(-0.031638, 0.059122, -0.997749), (0.039476, 0.997544, 0.057858), (0.99872, -0.037556, -0.033894)134.396881, -6.56577, 138.498611
13given(1), (1), (1)
14given(0.03119, 0.049698, 0.998277), (-0.01164, 0.998713, -0.049356), (-0.999446, -0.010081, 0.031728)-135.816925, 7.88202, 129.858261
15given(1), (1), (1)
16given(-0.436139, -0.068025, 0.897304), (-0.075337, 0.996398, 0.038919), (-0.89672, -0.050626, -0.439693)-53.76273, -16.14142, 126.677361
17given(1), (1), (1)
18given(-0.999994, -0.003296, 0.000888), (-0.003291, 0.999981, 0.00513), (-0.000905, 0.005127, -0.999986)136.5504, 0.01465, 132.750351
19given(1), (1), (1)
20given(-0.00842, -0.028415, 0.999561), (0.04115, 0.99874, 0.028738), (-0.999118, 0.041374, -0.00724)2.00645, -4.02642, 135.698395
21given(1), (1), (1)
22given(0.000343, -0.040485, -0.99918), (-0.045784, 0.998132, -0.040458), (0.998951, 0.045761, -0.001511)134.273651, 6.35683, -1.29441
23given(1), (1), (1)
24given(-0.909938, 0.022946, -0.414109), (0.014376, 0.999613, 0.0238), (0.414495, 0.015703, -0.909916)124.472328, -11.41323, 189.084976
25given(1), (1), (1)
26given(0.909433, -0.00591, 0.415809), (0.013916, 0.999772, -0.016226), (-0.415618, 0.020543, 0.909307)11.90939, -6.03267, -57.08847
27given(1), (1), (1)
28given(0.437322, -0.078868, 0.89584), (0.065386, 0.996299, 0.055793), (-0.896925, 0.034175, 0.44086)-89.668999, 2.81447, 168.717285
29given(1), (1), (1)
30given(0.896521, -0.099467, -0.431691), (0.092035, 0.995025, -0.038133), (0.433336, -0.005544, 0.901215)-33.318748, 7.75459, 46.545292
31given(1), (1), (1)
32given(-0.892436, -0.099393, 0.440089), (-0.09726, 0.99488, 0.027462), (-0.440566, -0.018295, -0.897534)31.041809, 16.218479, 225.853683
33given(1), (1), (1)
34given(0.024067, -0.099359, 0.994761), (0.0546, 0.993694, 0.097932), (-0.998218, 0.051957, 0.02934)-134.05722, -10.57042, 132.688293
35given(1), (1), (1)
36given(-0.024728, -0.090869, -0.995556), (-0.026573, 0.995568, -0.09021), (0.999341, 0.024225, -0.027033)135.384735, 14.86315, 140.071243
37given(1), (1), (1)
38given(0.009548, 0.025291, -0.999635), (0.036106, 0.99902, 0.02562), (0.999302, -0.036338, 0.008625)134.539719, -3.60475, -3.1192
39given(1), (1), (1)
40given(-0.001482, 0.037295, 0.999303), (-0.040873, 0.998467, -0.037324), (-0.999163, -0.040899, 4.5E-5)2.41496, 5.68829, 134.087799
41given(1), (1), (1)
42given(0.90939, -0.025943, 0.415134), (0.019173, 0.999607, 0.020468), (-0.415502, -0.010654, 0.90953)12.03386, -11.09854, -56.392132
43given(1), (1), (1)
44given(-0.909002, 0.002963, -0.416781), (0.009074, 0.999878, -0.012682), (0.416692, -0.015309, -0.908919)124.862823, -6.65503, 189.677444
45given(1), (1), (1)
46given(-0.999953, -0.005303, 0.008128), (-0.005398, 0.999917, -0.011727), (-0.008065, -0.01177, -0.999898)136.181442, 1.02207, 133.487366
47given(1), (1), (1)
48given(-0.405952, 0.025253, 0.913545), (0.05727, 0.998356, -0.002148), (-0.912098, 0.051447, -0.406731)-54.672661, -8.64487, 121.823334
49given(1), (1), (1)
50given(0.408372, 0.020851, -0.912578), (-0.029452, 0.99952, 0.009658), (0.91234, 0.022933, 0.40879)192.432114, -10.26866, 11.19982
51given(1), (1), (1)
52given(0.41306, -0.030269, -0.910201), (0.070178, 0.997534, -0.001325), (0.907996, -0.063328, 0.414165)190.991241, -8.60633, 10.22421
53given(1), (1), (1)
54given(-0.415491, -0.026401, 0.909214), (-0.042348, 0.999056, 0.009658), (-0.908611, -0.03449, -0.416217)-55.206501, -10.14428, 122.854317
55given(1), (1), (1)
56given(-0.999613, 0.027745, -0.001969), (0.027729, 0.999587, 0.00759), (0.002179, 0.007533, -0.999969)0.51396, -1.06696, 270.737701

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Components

#1: Protein
FAD:protein FMN transferase / Flavin transferase


Mass: 36017.258 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri ATCC 14405 = CCUG 16156 (bacteria)
Gene: CXK99_00610 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2N8RKH1, FAD:protein FMN transferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5 28% polyethylene glycol 2000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→138.06 Å / Num. obs: 104767 / % possible obs: 100 % / Redundancy: 6.9 % / Net I/σ(I): 2.7

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Processing

SoftwareName: REFMAC / Version: 5.8.0155 / Classification: refinement
RefinementResolution: 2.6→138.06 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU B: 32.48 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.533 / ESU R Free: 0.314 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27394 5134 4.9 %RANDOM
Rwork0.23187 ---
obs0.23392 99638 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.044 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å2-0 Å20.75 Å2
2---1.24 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.6→138.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18672 0 8 45 18725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01918990
X-RAY DIFFRACTIONr_bond_other_d0.0040.0218068
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.97525701
X-RAY DIFFRACTIONr_angle_other_deg1.12341587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62452448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15924.277844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.932153135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.35315135
X-RAY DIFFRACTIONr_chiral_restr0.10.22900
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02121748
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024143
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_it3.9374.9219867
X-RAY DIFFRACTIONr_mcbond_other3.9374.9219866
X-RAY DIFFRACTIONr_mcangle_it6.4067.36112290
X-RAY DIFFRACTIONr_mcangle_other6.4067.36212291
X-RAY DIFFRACTIONr_scbond_it3.8835.4039123
X-RAY DIFFRACTIONr_scbond_other3.8835.4049124
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4517.92513412
X-RAY DIFFRACTIONr_long_range_B_refined12.31491.51176300
X-RAY DIFFRACTIONr_long_range_B_other12.31491.51176301
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
1H2232TIGHT POSITIONAL0.150.13
1H2243TIGHT POSITIONAL0.190.13
1H2252TIGHT POSITIONAL0.180.13
1H2241TIGHT POSITIONAL0.180.13
1H2177TIGHT POSITIONAL0.20.13
1H2261TIGHT POSITIONAL0.190.13
1H2246TIGHT POSITIONAL0.20.13
1H2261TIGHT POSITIONAL0.20.13
1H2261TIGHT POSITIONAL0.230.13
1H2250TIGHT POSITIONAL0.160.13
1H2252TIGHT THERMAL8.511.32
2H2261TIGHT POSITIONAL0.20.13
2H2270TIGHT POSITIONAL0.180.13
2H2259TIGHT POSITIONAL0.170.13
2H2319TIGHT POSITIONAL0.130.13
2H2334TIGHT POSITIONAL0.180.13
2H2334TIGHT POSITIONAL0.20.13
2H2330TIGHT POSITIONAL0.210.13
2H2319TIGHT POSITIONAL0.220.13
2H2377TIGHT POSITIONAL0.210.13
2H2261TIGHT THERMAL8.361.32
3H2270TIGHT THERMAL8.51.32
4H2334TIGHT THERMAL6.141.32
5H2330TIGHT THERMAL6.681.32
6H2388TIGHT THERMAL6.811.32
7H2377TIGHT THERMAL8.751.32
8B2159TIGHT THERMAL11.931.32
9B2288TIGHT THERMAL4.31.32
10B2232TIGHT THERMAL6.841.32
11B2243TIGHT THERMAL6.431.32
12B2252TIGHT THERMAL8.061.32
13B2241TIGHT THERMAL6.171.32
14G2177TIGHT THERMAL12.351.32
15G2261TIGHT THERMAL8.031.32
16G2246TIGHT THERMAL8.831.32
17G2261TIGHT THERMAL9.481.32
18G2261TIGHT THERMAL9.771.32
19A2250TIGHT THERMAL7.021.32
20A2261TIGHT THERMAL6.651.32
21A2270TIGHT THERMAL7.31.32
22A2259TIGHT THERMAL6.921.32
23C2319TIGHT THERMAL3.641.32
24C2334TIGHT THERMAL6.221.32
25C2334TIGHT THERMAL6.741.32
26D2330TIGHT THERMAL6.091.32
27D2319TIGHT THERMAL6.041.32
28E2377TIGHT THERMAL6.821.32
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 404 -
Rwork0.376 7281 -
obs--100 %
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)
10.5834-0.04860.5760.14690.24081.1796-0.0228-0.04530.09070.0339-0.0515-0.02710.0528-0.16070.07430.0809-0.0036-0.04620.0272-0.00490.070830.6748.2802140.0531
20.25120.1413-0.06240.3740.00440.49210.01370.03010.00930.0428-0.018-0.0292-0.0419-0.05860.00430.1005-0.0039-0.02530.0130.00950.051477.6668-0.029395.994
30.22140.06610.73490.12840.09322.8868-0.06550.11360.0119-0.06790.03160.0731-0.41640.54140.03390.1467-0.1115-0.06030.12440.01280.054-31.55377.4604131.1647
40.2936-0.1495-0.2160.56520.11450.2484-0.0162-0.061-0.0055-0.0621-0.02790.03930.03730.0840.04420.0980.0444-0.03890.0430.00320.050459.0641-0.028536.6327
50.513-0.1610.33410.2315-0.10470.64360.0510.150.09770.0353-0.1112-0.00240.02940.07890.06020.0480.00670.03510.06660.01590.096938.5584-0.323975.3107
60.59730.08090.150.26490.14090.47160.0198-0.06340.0613-0.0348-0.0862-0.00310.0091-0.04510.06640.0370.01010.02510.03080.00270.078397.9740.001957.2435
70.32340.0255-0.18530.13050.11570.56790.0002-0.0326-0.0402-0.0274-0.0011-0.08550-0.14430.00090.05140.00730.0310.0887-0.0180.06935.42638.6179104.2927
80.78940.0539-0.70780.3393-0.30660.940.00290.13530.06830.07040.0640.0193-0.0364-0.1015-0.0670.0511-0.00950.01770.08360.00590.029-5.01658.4513166.5817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H29 - 348
2X-RAY DIFFRACTION2B29 - 348
3X-RAY DIFFRACTION3G29 - 345
4X-RAY DIFFRACTION4A29 - 348
5X-RAY DIFFRACTION5C29 - 348
6X-RAY DIFFRACTION6D29 - 348
7X-RAY DIFFRACTION7E29 - 348
8X-RAY DIFFRACTION8F29 - 348

+
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