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- PDB-5mr6: XiaF from Streptomyces sp. in complex with FADH2 and Glycerol -

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Basic information

Entry
Database: PDB / ID: 5mr6
TitleXiaF from Streptomyces sp. in complex with FADH2 and Glycerol
ComponentsXiaF protein
KeywordsOXIDOREDUCTASE / detoxification / non-canonical flavin-dependent terpenoid cyclase / xenobiotics-degrading enzyme / indigo / indirubin
Function / homology
Function and homology information


fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / XiaF protein
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKugel, S. / Baunach, M. / Baer, P. / Ishida-Ito, M. / Sundaram, S. / Xu, Z. / Groll, M. / Hertweck, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB749 Germany
CitationJournal: Nat Commun / Year: 2017
Title: Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification.
Authors: Kugel, S. / Baunach, M. / Baer, P. / Ishida-Ito, M. / Sundaram, S. / Xu, Z. / Groll, M. / Hertweck, C.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XiaF protein
B: XiaF protein
C: XiaF protein
D: XiaF protein
E: XiaF protein
F: XiaF protein
G: XiaF protein
H: XiaF protein
I: XiaF protein
J: XiaF protein
K: XiaF protein
L: XiaF protein
M: XiaF protein
N: XiaF protein
O: XiaF protein
P: XiaF protein
Q: XiaF protein
R: XiaF protein
S: XiaF protein
T: XiaF protein
U: XiaF protein
V: XiaF protein
W: XiaF protein
X: XiaF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,082,81772
Polymers1,061,75424
Non-polymers21,06348
Water84,2924679
1
E: XiaF protein
F: XiaF protein
G: XiaF protein
H: XiaF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,47012
Polymers176,9594
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: XiaF protein
J: XiaF protein
K: XiaF protein
L: XiaF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,47012
Polymers176,9594
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: XiaF protein
N: XiaF protein
O: XiaF protein
P: XiaF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,47012
Polymers176,9594
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
Q: XiaF protein
R: XiaF protein
S: XiaF protein
T: XiaF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,47012
Polymers176,9594
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
U: XiaF protein
V: XiaF protein
W: XiaF protein
X: XiaF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,47012
Polymers176,9594
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: XiaF protein
B: XiaF protein
C: XiaF protein
D: XiaF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,47012
Polymers176,9594
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.930, 167.090, 200.940
Angle α, β, γ (deg.)89.96, 90.18, 119.82
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T
211U
221V
231W
241X

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 400
2111B1 - 400
3111C1 - 400
4111D1 - 400
5111E1 - 400
6111F1 - 400
7111G1 - 400
8111H1 - 400
9111I1 - 400
10111J1 - 400
11111K1 - 400
12111L1 - 400
13111M1 - 400
14111N1 - 400
15111O1 - 400
16111P1 - 400
17111Q1 - 400
18111R1 - 400
19111S1 - 400
20111T1 - 400
21111U1 - 400
22111V1 - 400
23111W1 - 400
24111X1 - 400

NCS oper:
IDCodeMatrixVector
1given(1, 1), (1, 1), (1)1
2given(2, -0.999996, -0.002745), (2, 0.002748, -0.999987), (2, 0.000765, 0.004357)0.000777, 0.004355, 0.99999
3given(3, -0.496775, -0.867875), (3, -0.86788, 0.496771), (3, 0.000144, -0.003307)0.002798, -0.001767, -0.999995
4given(4, 0.497612, 0.867399), (4, 0.867398, -0.497613), (4, -0.001763, -0.000279)-0.00112, -0.00139, -0.999998
5given(5, 0.999987, -0.004969), (5, 0.00497, 0.999987), (5, 0.000699, -0.000874)-0.000703, 0.000871, 0.999999
6given(6, -0.999995, 0.002958), (6, -0.002953, -0.999986), (6, 0.001035, 0.004469)0.001022, 0.004472, 0.999989
7given(7, -0.500944, -0.865478), (7, -0.865479, 0.500945), (7, -0.000676, -0.001554)0.001683, -0.000194, -0.999999
8given(8, 0.502796, 0.864405), (8, 0.864404, -0.502797), (8, -0.001479, -3.6E-5)-0.000775, -0.001261, -0.999999
9given(9, 0.496934, -0.867788), (9, -0.867779, -0.496932), (9, 0.003985, 0.001589)0.000601, -0.004247, -0.999991
10given(10, -0.49551, 0.8686), (10, 0.868598, 0.495513), (10, 0.002782, -0.000759)-0.002038, 0.00204, -0.999996
11given(11, 0.508448, 0.861088), (11, -0.86108, 0.508456), (11, -0.004674, -0.00072)0.002996, -0.003658, 0.999989
12given(12, -0.507972, -0.861367), (12, 0.861355, -0.507982), (12, -0.00561, -0.00052)-0.003298, 0.004568, 0.999984
13given(13, 0.499456, -0.866338), (13, -0.866329, -0.499458), (13, 0.00432, 0.000673)0.001575, -0.004079, -0.99999
14given(14, -0.498841, 0.866687), (14, 0.866684, 0.49885), (14, 0.00411, -0.001517)-0.003365, 0.002806, -0.99999
15given(15, 0.507552, 0.861618), (15, -0.861603, 0.507557), (15, -0.005602, 0.000738)0.002208, -0.005201, 0.999984
16given(16, -0.504714, -0.863284), (16, 0.863274, -0.504719), (16, -0.004705, 2.4E-5)-0.002354, 0.004074, 0.999989
17given(17, -0.999985, -0.005134), (17, -0.005142, 0.99998), (17, 0.002077, 0.003683)-0.002096, 0.003673, -0.999991
18given(18, 0.999995, 0.001216), (18, 0.001228, -0.99999), (18, 0.00283, 0.004287)0.002835, -0.004284, -0.999987
19given(19, 0.49807, -0.867136), (19, 0.867136, 0.498068), (19, -0.000902, -0.00187)-0.001172, 0.001714, 0.999998
20given(20, -0.499699, 0.866198), (20, -0.866198, -0.499697), (20, -0.001277, -0.001954)0.001054, -0.002083, 0.999997
21given(21, -0.999984, -0.005103), (21, -0.00511, 0.999983), (21, 0.002298, 0.00289)-0.002313, 0.002879, -0.999993
22given(22, 0.999983, 0.004511), (22, 0.00453, -0.999975), (22, 0.00355, 0.005395)0.003575, -0.005379, -0.999979
23given(23, 0.500445, -0.865767), (23, 0.865766, 0.500441), (23, -0.001816, -0.002288)-0.001073, 0.002717, 0.999996
24given(24, -0.502269, 0.864711), (24, -0.86471, -0.502268), (24, -0.001237, -0.001236)0.000447, -0.00169, 0.999998

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Components

#1: Protein ...
XiaF protein


Mass: 44239.750 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: xiaF / Production host: Escherichia coli (E. coli) / References: UniProt: I7IIA9
#2: Chemical...
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4679 / 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: 4.59 Å3/Da / Density % sol: 73.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M (NH4)2SO4, 0.1 M HEPES, 0.1 M NaCl, 0.1 M NADH, 0.15 M FAD, 10% Glycerol, anaerobic crystallization 0.0005 mM XiaP (protein, reductase)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 703582 / % possible obs: 95.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.4
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LVW
Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 16.185 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22881 35038 5 %RANDOM
Rwork0.19822 ---
obs0.19975 665721 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.471 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.62 Å2-1.62 Å2
2--1.08 Å20.59 Å2
3----3.16 Å2
Refinement stepCycle: 1 / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms71448 0 1416 4679 77543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01974424
X-RAY DIFFRACTIONr_bond_other_d0.0020.0268856
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.975101688
X-RAY DIFFRACTIONr_angle_other_deg1.0453158232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.90659480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93422.4223072
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1921511064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.06615720
X-RAY DIFFRACTIONr_chiral_restr0.0850.211712
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02183760
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0215768
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_it2.8843.19137992
X-RAY DIFFRACTIONr_mcbond_other2.8813.19137991
X-RAY DIFFRACTIONr_mcangle_it3.8164.77947448
X-RAY DIFFRACTIONr_mcangle_other3.8164.77947449
X-RAY DIFFRACTIONr_scbond_it3.5593.68836432
X-RAY DIFFRACTIONr_scbond_other3.5583.68836432
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3695.3654241
X-RAY DIFFRACTIONr_long_range_B_refined5.12661.422325830
X-RAY DIFFRACTIONr_long_range_B_other4.9861.347322664
X-RAY DIFFRACTIONr_rigid_bond_restr2.9313143280
X-RAY DIFFRACTIONr_sphericity_free31.56651814
X-RAY DIFFRACTIONr_sphericity_bonded14.2765144585
Refine LS restraints NCS

Ens-ID: 1 / Number: 5814 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A5.22
2B5.42
3C5.31
4D5.27
5E5.44
6F4.85
7G5.45
8H6.03
9I5.93
10J5.64
11K5.21
12L6.16
13M5.28
14N5.89
15O6.66
16P5.73
17Q6.21
18R5.26
19S5.87
20T5.73
21U5.42
22V5.87
23W5.65
24X5.63
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 2522 -
Rwork0.358 47912 -
obs--94.74 %
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)
10.03090.0237-0.01080.0923-0.03550.0638-0.00280.0139-0.00480.00130.0057-0.0056-0.01490.0074-0.00290.048-0.02040.06330.0142-0.02510.088353.7347-54.2199-1.241
20.03030.0274-0.00560.0435-0.01350.0528-0.00030.0020.0057-0.0040.0030.00270.0094-0.0018-0.00270.0437-0.0210.06030.0104-0.02940.088230.6645-88.608-1.1667
30.05570.0102-0.0260.00950.01780.10270.0035-0.0114-0.0015-0-0.00130-0.0054-0.0046-0.00220.0403-0.01680.06190.0141-0.02430.096121.5957-72.864635.0752
40.03510.00980.03830.00290.00910.0730.0068-0.00720.00730.0013-0.00280.0007-0.00250.0149-0.00390.0345-0.01870.05660.0215-0.02740.094362.8042-69.826735.0375
50.05530.0216-0.01050.0152-0.02790.09050.00370.0079-0.00280.00710.00040.0039-0.01230.0046-0.00410.0448-0.01860.06160.0102-0.02630.08764.6487-47.869493.5361
60.00790.00060.0140.01770.00030.0260.004-0.0010.002-0.00230.00490.00650.00250.0017-0.00890.0445-0.0230.06040.0138-0.02960.09241.3975-82.119293.6082
70.07380.0182-0.01570.0055-0.01130.0650.0065-0.0104-0.0001-0.00070.0021-0.0022-0.0015-0.0203-0.00850.0433-0.01850.06420.0242-0.02280.097632.4288-66.3792129.8514
80.07380.01040.01540.0031-0.01040.1040.003-0.00420.00240.0006-0.00330.00050.0020.01230.00040.0387-0.02030.05970.0159-0.03090.092573.6611-63.5618129.817
90.04290.0011-0.01940.00890.00910.07370.00290.0022-0.00460.00050.0005-0.0020.0019-0.0071-0.00340.0453-0.01920.06230.0088-0.02640.088974.3725-17.7081169.0884
100.01370.01720.02730.03150.0510.085-0.0012-0.0014-0.00010.00180.00020.0079-0.00670.00340.00090.0455-0.0180.06150.0083-0.02410.084292.707119.4252169.1636
110.0581-0.02410.06330.0491-0.04260.1045-0.0013-0.00560.01-0.0018-0.0012-0.0059-0.0069-0.01750.00250.0444-0.01410.06140.0132-0.02170.087174.809719.5658132.8243
120.0063-0.0137-0.01830.03020.04020.05360.00350.00020.0027-0.0011-0.00130.0001-0.0039-0.0021-0.00220.0425-0.01950.06180.0092-0.02860.090192.5454-17.7641132.8899
130.01290.0162-0.02740.0527-0.02420.072-0.0004-0.00150.0036-0.00210.0087-0.00450.0092-0.0011-0.00830.0475-0.01960.0610.0131-0.02430.08985.9735-11.163362.8986
140.02460.00560.02930.0414-0.00790.0986-0.00230.00110.00230.0090.0020.0003-0.01290.01070.00030.0452-0.01980.06070.0104-0.02780.0882104.168126.025162.9617
150.0216-0.01410.0510.0333-0.03170.1245-0.002-0.00370.001-0.00280.0022-0.00730.0007-0.0116-0.00010.0416-0.01510.06180.0076-0.02170.092886.314726.088626.5984
160.0138-0.0241-0.01360.0546-0.00120.06970.0066-0.00060.0034-0.0134-0.00570.00370.01530.0099-0.00090.0469-0.01440.05860.0101-0.02730.0886104.1582-11.206726.6979
170.0188-0.02710.01810.07520.01080.0663-0.00180.0016-0.00320.00550.0010.0117-0.0052-0.00260.00080.0419-0.01650.06390.0129-0.02630.0988113.9636-54.3171102.1053
180.0109-0.01750.01950.0668-0.03280.08340.00120.00130.00240.00530.0004-0.00360.01540.0111-0.00170.0466-0.01410.0610.0096-0.02660.0924137.1605-88.5257102.0457
190.1056-0.0046-0.05440.0112-0.01840.07040.00660.0072-0.0051-0.0064-0.00050.00060.00410.0077-0.00610.0429-0.01790.06070.0226-0.03410.0971146.2652-72.80565.8211
200.07150.0110.02970.0116-0.01910.08190.0001-0.00070.009-0.0050.0027-0.00250.0026-0.0167-0.00280.0366-0.01590.0580.0231-0.02520.0947105.0518-69.856965.7633
210.0031-0.00620.00950.06460.00960.0492-0.00450.0026-0.00470.00210.00010.0064-0.01110.00340.00440.0437-0.01220.06010.018-0.02230.0924124.7807-47.9402196.8617
220.0209-0.01950.03490.0723-0.04130.06080.0043-0.00010.0040.0021-0.0032-0.0084-0.00070.0024-0.00110.0407-0.01430.05880.0139-0.02180.0885148.0328-82.0963196.7919
230.0697-0.0092-0.02750.016-0.01630.04090.00210.0059-0.00270.002-0.00030.0041-0.00130.0067-0.00180.0422-0.01460.06230.031-0.02650.0931157.1164-66.3446160.5852
240.05740.02740.04550.0230.00690.08040.00280.00150.0112-0.00620.0035-0.0048-0.0028-0.013-0.00630.0388-0.01590.05950.0257-0.0230.0921115.8904-63.5264160.5267
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 602
2X-RAY DIFFRACTION2B2 - 602
3X-RAY DIFFRACTION3C2 - 602
4X-RAY DIFFRACTION4D2 - 602
5X-RAY DIFFRACTION5E2 - 602
6X-RAY DIFFRACTION6F2 - 602
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