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- PDB-4lty: Crystal Structure of E.coli SbcD at 1.8 A Resolution -

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Basic information

Entry
Database: PDB / ID: 4lty
TitleCrystal Structure of E.coli SbcD at 1.8 A Resolution
ComponentsExonuclease subunit SbcD
KeywordsHYDROLASE / meiotic recombination 11 homolog / double-strand break repair protein / nuclease / endonuclease / exonuclease
Function / homologyDouble Stranded RNA Binding Domain - #720 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Double Stranded RNA Binding Domain / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLiu, S. / Tian, L.F. / Yan, X.X. / Liang, D.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis for DNA recognition and nuclease processing by the Mre11 homologue SbcD in double-strand breaks repair.
Authors: Liu, S. / Tian, L.F. / Liu, Y.P. / An, X.M. / Tang, Q. / Yan, X.X. / Liang, D.C.
History
DepositionJul 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Exonuclease subunit SbcD
B: Exonuclease subunit SbcD
A: Exonuclease subunit SbcD
D: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,2398
Polymers157,8704
Non-polymers3684
Water15,223845
1
C: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5602
Polymers39,4681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5602
Polymers39,4681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5602
Polymers39,4681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Exonuclease subunit SbcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5602
Polymers39,4681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.138, 69.359, 95.023
Angle α, β, γ (deg.)72.21, 84.10, 83.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Exonuclease subunit SbcD / Nuclease SbcCD / D subunit


Mass: 39467.609 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 15-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: sbcD, EKO11_3451, KO11_21615 / Production host: Escherichia coli (E. coli) / References: UniProt: E8Y9D8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 845 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97917 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 133390

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.857 Å / SU ML: 0.19 / σ(F): 1.96 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 6634 4.98 %
Rwork0.156 --
obs0.1578 133143 95.96 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.041 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3684 Å20.6021 Å23.8803 Å2
2---1.547 Å21.0484 Å2
3----1.8214 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10193 0 24 845 11062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810739
X-RAY DIFFRACTIONf_angle_d1.1814737
X-RAY DIFFRACTIONf_dihedral_angle_d15.5183769
X-RAY DIFFRACTIONf_chiral_restr0.0821714
X-RAY DIFFRACTIONf_plane_restr0.0051939
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82040.27912300.2306420795
1.8204-1.84180.24452160.208420996
1.8418-1.86430.24942410.1875420696
1.8643-1.88790.25162130.1788418996
1.8879-1.91270.19912250.1625419696
1.9127-1.93890.22192050.1578428396
1.9389-1.96660.23532390.1609415596
1.9666-1.99590.20442390.1553427896
1.9959-2.0270.20132200.1512422497
2.027-2.06020.19852270.1504424397
2.0602-2.09570.20952170.153422397
2.0957-2.13380.19612380.1507425597
2.1338-2.17480.19582140.1534422797
2.1748-2.21910.20192200.1501432297
2.2191-2.26730.1952380.1479420297
2.2673-2.320.20362260.1479428597
2.32-2.37790.19932110.1494427697
2.3779-2.44210.20552140.1536422497
2.4421-2.51380.20492100.1509434897
2.5138-2.59480.18152320.1458423197
2.5948-2.68730.20912320.1507426597
2.6873-2.79460.21382240.1676425597
2.7946-2.92140.21592200.1714426697
2.9214-3.07490.20142150.1674429397
3.0749-3.26680.18952420.1577425097
3.2668-3.51770.18892360.1523417096
3.5177-3.86940.16652050.1431405992
3.8694-4.42390.15972020.1383400191
4.4239-5.55330.15332040.1368411294
5.5533-19.85820.1861790.1857405591
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)
13.33741.1786-1.1398.5047-3.43995.04650.2087-0.31830.21210.0703-0.1732-0.2407-0.44970.82520.00540.2284-0.07890.04850.2545-0.08920.127815.04164.44556.558
22.1483-0.1551-0.65593.7053-2.16484.89260.0537-0.00790.1662-0.146-0.0305-0.2591-0.21580.4229-0.02520.1577-0.03770.02560.1297-0.04510.140316.79168.76362.038
39.4545-8.01263.73939.3078-0.26076.54590.0482-0.2334-0.2015-0.2223-0.4599-0.62510.4941.71010.43990.2630.08830.05780.45860.06810.186314.24661.14468.589
46.8209-4.55880.30046.5822-1.15948.5081-0.05880.008-0.272-0.12790.0412-0.00610.44160.2063-0.0010.1554-0.03790.03130.1007-0.00690.13723.49570.76767.762
55.27451.04023.58233.12782.06593.0512-0.10250.56-0.37690.08190.3977-0.36820.50590.5975-0.25870.30940.04550.09010.295-0.05390.259132.65660.75566.948
64.3171-1.28170.07076.2376-0.76163.85060.07260.21610.0237-0.15250.14130.482-0.0766-0.5779-0.19270.17770.01160.06040.2570.02470.149235.75374.44955.446
75.0643-0.2972-1.57315.9112-1.10063.85560.2543-0.28060.33450.40790.07740.3719-0.6028-0.261-0.30280.23150.02390.08160.1996-0.00560.151131.45269.2247.59
81.8057-0.42060.33458.5453-1.89460.53140.1298-0.52660.37760.66020.0777-0.2384-0.9880.323-0.19240.584-0.10210.10760.2411-0.15130.221718.00464.54147.568
96.91426.1625-3.33682.0997-4.30843.6748-0.0804-0.7433-0.11290.2249-0.0292-0.3934-0.5540.89460.12410.4929-0.18510.11880.4147-0.13250.291120.03358.2649.509
101.6985-1.14560.6034.89321.52211.139-0.3525-0.39930.68070.39360.0781-0.4423-0.67130.34890.09551.7401-0.69450.1867-0.1047-0.6230.3724-2.61872.63236.962
111.3838-0.40850.06733.6730.54911.6188-0.22530.1815-0.1032-0.76270.2914-0.53940.30350.0784-0.04161.5767-0.13560.19630.4881-0.12230.8422-3.58184.65935.402
122.87282.53882.33364.4761.36222.108-0.21480.0819-0.15770.09450.1369-0.5613-0.60570.4142-0.06881.4156-0.29210.27360.2566-0.17190.5589-3.65476.4442.808
131.8002-0.36190.02081.8990.84425.45540.04760.08630.0924-0.0408-0.02840.1684-0.0443-0.42830.00440.1184-0.00590.03480.15780.04540.152531.074971.6652119.21
148.15317.4632-5.88656.8626-4.97028.9688-0.06890.0298-0.0710.1660.07970.12380.1312-0.1208-0.07770.22370.0140.0130.1273-0.00330.16732.526259.6478125.3433
159.87526.58313.10598.17472.55731.80570.1134-0.3638-0.34240.2107-0.1561-0.01660.5325-0.18510.04460.25960.00730.06690.20.04170.15939.802957.8369116.0244
169.572-6.91585.39957.1318-2.97753.4305-0.1267-0.7308-0.15920.41490.125-0.95770.53460.64390.0040.32970.1686-0.07060.59110.12510.527663.630860.3219125.9367
172.01737.93431.86762.0117-1.32739.6257-0.1836-0.0321-1.0363-0.4943-0.0022-1.05631.01260.73430.1750.25180.14060.07290.28310.03670.405454.345659.5835115.21
184.72662.65570.47477.59082.26784.83190.08710.0465-0.1437-0.0739-0.1185-0.33330.24720.15320.02350.11630.03630.02840.18460.05030.118346.946665.2187112.1892
195.0921-2.1326-2.4212.80611.26634.01150.09590.36710.2011-0.2175-0.0912-0.2084-0.12290.19270.00820.1553-0.01380.04940.19340.05550.150646.683371.5015108.9701
201.34122.09652.33696.7444.74144.4259-0.19760.38540.4314-0.9992-0.0269-0.0596-0.51930.59790.23360.635-0.01450.17360.3080.1590.542138.212188.1469111.016
211.48230.39180.37567.8735-0.69580.54950.10260.28530.368-0.79120.0424-0.0326-0.8489-0.161-0.16640.51890.02620.07590.29450.12290.250833.67583.1834106.7391
222.29544.316-1.00188.1259-1.92484.9433-0.45940.83890.9684-0.57290.40030.4869-1.0294-0.62880.07920.85010.15060.05990.37440.18250.57427.460998.1119115.1035
232.4125-0.88970.08916.97050.56551.2077-0.173-0.11190.04250.33630.0123-0.4224-0.27620.09580.12671.78120.10280.34020.43920.02641.135939.8403108.7333121.3721
243.70042.67132.51451.9341.96027.9769-0.2317-0.14241.38360.1319-0.2983-0.1806-1.0524-0.40.47640.71450.04630.11720.23460.02270.578330.830699.9278119.6412
252.01331.9783-7.32331.99719.03656.7199-0.2475-0.1633-0.9915-0.4140.03390.85410.39950.0383-0.0150.28180.0131-0.02310.1218-0.01950.294613.28964.019104.294
263.145-2.4891-0.10723.95120.19050.5675-0.0172-0.0638-0.04510.11070.05730.17050.0494-0.0157-0.04170.1549-0.02310.0290.07620.00340.109315.33582.46286.187
272.14834.3022-2.7929.713-5.52564.54630.0589-0.0713-0.04020.2354-0.0877-0.1712-0.00560.09490.03130.12470.01450.00050.1099-0.01640.121112.30374.52982.928
288.4953-9.1791-1.52032.0188-0.84599.5935-0.3765-0.37650.14341.1340.1222-0.0396-0.04410.20130.25240.2385-0.0419-0.03080.17960.01480.186812.7267.28878.296
291.6689-2.15410.6454.5799-3.50814.2966-0.0634-0.15460.22920.26150.0336-0.5388-0.15580.14740.04050.1231-0.0105-0.00590.1491-0.0250.22933.1167.92188.135
302.73421.6196-2.13081.2541-0.41984.04240.2127-0.36071.63720.0569-0.7436-1.4-2.43941.58520.520.7885-0.2670.01050.6189-0.03241.1227-14.86874.12880.331
314.91133.1812-0.94772.0552-8.7819.88720.22820.05150.57380.3039-0.3481-0.9494-0.49080.81350.21660.2481-0.05010.09810.2414-0.01120.4959-11.6773.23189.947
322.2709-0.81740.00653.1826-0.35080.84670.0340.17840.1156-0.3099-0.0427-0.40630.01480.10450.01660.1909-0.01860.06510.1125-0.0040.16641.23279.73296.098
332.71340.03760.98841.3979-1.06221.98480.41560.8556-0.6168-0.8153-0.21620.77630.1275-0.2725-0.21610.47660.0485-0.14110.411-0.090.2316.06598.23496.635
342.03712.23544.40636.7254-0.37049.11750.07640.6748-0.9615-0.5127-0.00520.18260.722-0.9512-0.11840.28780.021-0.04570.3525-0.00460.376318.667103.67388.508
359.79175.8148-0.66885.9452-5.0258.6866-0.01660.01291.3453-0.74260.53281.9955-0.4574-1.095-0.53040.50210.1699-0.11240.55120.02560.824215.366116.07583.147
362.01027.17055.39468.1876-2.1332.015-0.08750.4811-0.73780.1067-0.0468-0.4266-0.7067-0.20620.16020.30940.0136-0.01120.26270.0090.344215.929106.04684.062
371.86250.71170.38231.63630.36930.8593-0.0260.0872-0.0196-0.0404-0.01190.06210.0191-0.02310.0360.14390.00290.03690.07950.0080.133822.1821101.295452.6849
382.9164-3.5564-0.17472.00276.52485.6197-0.13620.17620.2843-0.11020.33-0.66890.0825-0.2149-0.19960.1597-0.0156-0.00420.14910.04050.26676.0854101.467448.3384
391.68962.11530.48394.95943.7834.49570.00220.04750.4183-0.3186-0.08050.5622-0.3552-0.15220.07740.1250.0332-0.01870.13820.04110.25188.5318109.051553.0422
405.1815-1.76282.08292.0006-0.39682.00070.1271-0.1472.19060.7832-0.05011.2259-2.5003-1.4046-0.1530.72970.07230.25630.4492-0.14431.00834.4364129.557865.9437
417.25267.11734.12982.08627.82717.7065-0.1159-0.00220.4807-0.3144-0.22840.8918-0.2972-0.48850.40460.22230.0745-0.00770.18240.03790.4689-0.4063110.686156.8444
424.49052.94-1.00045.2659-0.12570.2638-0.1563-0.01080.19380.12820.15050.4981-0.07240.03930.0160.16730.04480.03830.07010.02490.191911.3457108.308363.2704
437.03485.7060.83069.33573.8492.48360.0556-0.32720.46950.1598-0.15050.7129-0.162-0.20350.11150.23560.01310.06990.1080.02680.17369.758109.341166.4138
444.6606-1.04590.05391.6850.80722.9287-0.2029-0.2526-0.14530.39670.01010.30950.1975-0.17240.17930.263-0.00230.07490.0812-0.00310.179617.3364102.996469.135
454.82120.87431.85441.91470.48922.79820.2129-0.8138-0.28160.5862-0.2398-0.2490.12780.204-0.01260.3442-0.0121-0.03090.2590.0640.181827.801597.351171.3495
466.7522.54790.43022.84750.24057.3489-0.1089-1.08630.02291.50330.2042-0.72680.16880.9322-0.1230.51150.0767-0.17670.5578-0.01560.315743.351106.039475.4748
477.09113.44241.34428.43422.16627.8111-0.052-0.0460.54130.83020.0589-2.3042-0.75492.2881-0.01980.5543-0.1219-0.28740.93780.04460.978951.953108.812876.5538
489.62273.25397.19919.474-1.33367.0783-0.0091-0.55050.30630.4587-0.79570.5078-0.60580.60430.80760.2733-0.0214-0.01290.3487-0.02160.241942.7471108.82272.9594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -2:36 )A-2 - 36
2X-RAY DIFFRACTION2( CHAIN A AND RESID 37:64 )A37 - 64
3X-RAY DIFFRACTION3( CHAIN A AND RESID 65:72 )A65 - 72
4X-RAY DIFFRACTION4( CHAIN A AND RESID 73:107 )A73 - 107
5X-RAY DIFFRACTION5( CHAIN A AND RESID 108:120 )A108 - 120
6X-RAY DIFFRACTION6( CHAIN A AND RESID 121:202 )A121 - 202
7X-RAY DIFFRACTION7( CHAIN A AND RESID 203:240 )A203 - 240
8X-RAY DIFFRACTION8( CHAIN A AND RESID 241:261 )A241 - 261
9X-RAY DIFFRACTION9( CHAIN A AND RESID 262:279 )A262 - 279
10X-RAY DIFFRACTION10( CHAIN A AND RESID 280:309 )A280 - 309
11X-RAY DIFFRACTION11( CHAIN A AND RESID 310:329 )A310 - 329
12X-RAY DIFFRACTION12( CHAIN A AND RESID 330:338 )A330 - 338
13X-RAY DIFFRACTION13( CHAIN B AND RESID -1:92 )B-1 - 92
14X-RAY DIFFRACTION14( CHAIN B AND RESID 93:107 )B93 - 107
15X-RAY DIFFRACTION15( CHAIN B AND RESID 108:135 )B108 - 135
16X-RAY DIFFRACTION16( CHAIN B AND RESID 136:153 )B136 - 153
17X-RAY DIFFRACTION17( CHAIN B AND RESID 154:164 )B154 - 164
18X-RAY DIFFRACTION18( CHAIN B AND RESID 165:202 )B165 - 202
19X-RAY DIFFRACTION19( CHAIN B AND RESID 203:244 )B203 - 244
20X-RAY DIFFRACTION20( CHAIN B AND RESID 245:252 )B245 - 252
21X-RAY DIFFRACTION21( CHAIN B AND RESID 253:296 )B253 - 296
22X-RAY DIFFRACTION22( CHAIN B AND RESID 297:310 )B297 - 310
23X-RAY DIFFRACTION23( CHAIN B AND RESID 311:328 )B311 - 328
24X-RAY DIFFRACTION24( CHAIN B AND RESID 330:338 )B330 - 338
25X-RAY DIFFRACTION25( CHAIN C AND RESID -2:2 )C-2 - 2
26X-RAY DIFFRACTION26( CHAIN C AND RESID 3:63 )C3 - 63
27X-RAY DIFFRACTION27( CHAIN C AND RESID 64:91 )C64 - 91
28X-RAY DIFFRACTION28( CHAIN C AND RESID 92:102 )C92 - 102
29X-RAY DIFFRACTION29( CHAIN C AND RESID 103:136 )C103 - 136
30X-RAY DIFFRACTION30( CHAIN C AND RESID 137:141 )C137 - 141
31X-RAY DIFFRACTION31( CHAIN C AND RESID 148:165 )C148 - 165
32X-RAY DIFFRACTION32( CHAIN C AND RESID 166:265 )C166 - 265
33X-RAY DIFFRACTION33( CHAIN C AND RESID 266:295 )C266 - 295
34X-RAY DIFFRACTION34( CHAIN C AND RESID 301:310 )C301 - 310
35X-RAY DIFFRACTION35( CHAIN C AND RESID 311:332 )C311 - 332
36X-RAY DIFFRACTION36( CHAIN C AND RESID 333:338 )C333 - 338
37X-RAY DIFFRACTION37( CHAIN D AND RESID -3:109 )D-3 - 109
38X-RAY DIFFRACTION38( CHAIN D AND RESID 110:117 )D110 - 117
39X-RAY DIFFRACTION39( CHAIN D AND RESID 118:140 )D118 - 140
40X-RAY DIFFRACTION40( CHAIN D AND RESID 141:151 )D141 - 151
41X-RAY DIFFRACTION41( CHAIN D AND RESID 152:173 )D152 - 173
42X-RAY DIFFRACTION42( CHAIN D AND RESID 174:201 )D174 - 201
43X-RAY DIFFRACTION43( CHAIN D AND RESID 202:225 )D202 - 225
44X-RAY DIFFRACTION44( CHAIN D AND RESID 226:247 )D226 - 247
45X-RAY DIFFRACTION45( CHAIN D AND RESID 248:298 )D248 - 298
46X-RAY DIFFRACTION46( CHAIN D AND RESID 299:317 )D299 - 317
47X-RAY DIFFRACTION47( CHAIN D AND RESID 318:331 )D318 - 331
48X-RAY DIFFRACTION48( CHAIN D AND RESID 332:340 )D332 - 340

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