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- PDB-8oro: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -

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Basic information

Entry
Database: PDB / ID: 8oro
TitleCRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) S101A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER HYPEROXYC CONDITIONS
Components1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
KeywordsOXIDOREDUCTASE / ALPHA-BETA HYDROLASE COMPLEX / DIOXYGENASE / COFACTOR-DEVOID
Function / homology
Function and homology information


3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / :
Similarity search - Function
alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
OXYGEN MOLECULE / D(-)-TARTARIC ACID / 2-methyl-quinolin-4(1H)-one / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
Similarity search - Component
Biological speciesPaenarthrobacter nitroguajacolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBui, S. / Steiner, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/I020411/1 United Kingdom
CitationJournal: Chem Sci / Year: 2023
Title: Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the alpha / beta-hydrolase fold.
Authors: Bui, S. / Gil-Guerrero, S. / van der Linden, P. / Carpentier, P. / Ceccarelli, M. / Jambrina, P.G. / Steiner, R.A.
History
DepositionApr 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
BBB: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,64512
Polymers66,5472
Non-polymers1,09810
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-1 kcal/mol
Surface area22290 Å2
Unit cell
Length a, b, c (Å)120.110, 120.110, 44.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 275 / Label seq-ID: 15 - 287

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase


Mass: 33273.391 Da / Num. of mol.: 2 / Mutation: C69S, S101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nitroguajacolicus (bacteria)
Gene: hod, meqE, ARUE_113p00080, pAL1.008 / Production host: Escherichia coli (E. coli)
References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase

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Non-polymers , 6 types, 420 molecules

#2: Chemical ChemComp-VFH / 2-methyl-quinolin-4(1H)-one


Mass: 159.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97932 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.854
pseudo-merohedral22-K, -H, -L20.146
ReflectionResolution: 2→60.05 Å / Num. obs: 43233 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.093 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3144 / Rpim(I) all: 0.406 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→60.05 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.873 / SU B: 6.504 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2687 2154 4.984 %
Rwork0.2274 41062 -
all0.229 --
obs-43216 98.868 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 28.482 Å2
Baniso -1Baniso -2Baniso -3
1-3.426 Å20 Å20 Å2
2--3.426 Å20 Å2
3----6.852 Å2
Refinement stepCycle: LAST / Resolution: 2→60.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 75 410 4937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134754
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154275
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.6416478
X-RAY DIFFRACTIONr_angle_other_deg1.1681.5879868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61821.557289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28115751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2561539
X-RAY DIFFRACTIONr_chiral_restr0.060.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021147
X-RAY DIFFRACTIONr_nbd_refined0.1840.21069
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.24207
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22205
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2377
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1670.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.290.225
X-RAY DIFFRACTIONr_nbd_other0.3030.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.29
X-RAY DIFFRACTIONr_mcbond_it0.3911.5882215
X-RAY DIFFRACTIONr_mcbond_other0.3911.5882216
X-RAY DIFFRACTIONr_mcangle_it0.6112.3792776
X-RAY DIFFRACTIONr_mcangle_other0.6112.3792775
X-RAY DIFFRACTIONr_scbond_it0.4011.6382539
X-RAY DIFFRACTIONr_scbond_other0.4011.6392540
X-RAY DIFFRACTIONr_scangle_it0.5952.4413695
X-RAY DIFFRACTIONr_scangle_other0.5952.4423696
X-RAY DIFFRACTIONr_lrange_it3.07230.67920842
X-RAY DIFFRACTIONr_lrange_other2.80630.27820550
X-RAY DIFFRACTIONr_ncsr_local_group_10.0580.059738
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.057830.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.057830.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3181520.2429710.24431830.9690.98398.1150.233
2.052-2.1080.2961550.22929520.23331170.9760.98599.67920.222
2.108-2.1690.2731470.2328380.23230190.9740.98398.87380.22
2.169-2.2350.3271390.22627390.23129600.9620.98197.22970.217
2.235-2.3080.2611450.21526910.21728480.9730.98399.57870.204
2.308-2.3890.2631320.21725990.21927520.9680.9899.23690.206
2.389-2.4790.2711340.23525410.23726780.9560.96999.8880.224
2.479-2.5790.2731240.22224360.22425710.9590.97299.57210.212
2.579-2.6930.271200.22523040.22724740.9570.9797.9790.212
2.693-2.8240.2441190.22422440.22523730.9590.96699.57860.212
2.824-2.9760.2631150.24221390.24322660.9450.9599.47040.233
2.976-3.1550.2621040.23220040.23421170.9360.95399.57490.224
3.155-3.370.2691000.23218950.23320100.9370.95199.25370.225
3.37-3.6380.296950.22417490.22818830.9120.95597.92880.22
3.638-3.9810.266850.21816330.22117370.9360.95398.90620.217
3.981-4.4430.238800.21514850.21715870.9430.95698.61370.215
4.443-5.1170.244680.22112980.22213960.9490.95497.8510.222
5.117-6.2340.262610.23911180.2412100.9580.95197.4380.244
6.234-8.6790.29500.258890.2529530.930.94398.53090.253
8.679-35.0050.268290.245370.2415770.9620.94898.09360.257
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)
112.0017-7.5257-4.321810.00294.32685.7267-0.3166-0.42870.15140.41280.3742-0.2420.15660.2146-0.05760.1844-0.0015-0.02230.15440.04890.1547-54.331325.988313.0757
22.10471.00422.514711.53441.69863.9632-0.00320.1163-0.3296-0.03330.2202-0.03580.23560.524-0.2170.24010.0046-0.01160.20860.07120.2591-47.25815.823.7763
33.4492-3.27241.43293.1698-1.54961.15640.0208-0.3734-0.0605-0.02450.31830.15290.0014-0.1067-0.33910.2611-0.0032-0.01740.12890.03920.2344-56.268125.03488.394
412.2288-11.38243.543912.151-6.878111.8919-0.2052-0.58370.67430.17630.1878-0.45010.4642-0.50350.01740.2566-0.17640.09080.6043-0.08110.3695-68.527324.46439.3454
51.8467-0.0896-0.85152.6167-0.4271.3439-0.0869-0.3702-0.1110.02230.10650.2340.1914-0.1244-0.01960.1159-0.0173-0.0470.17260.04140.0857-54.747632.28172.2397
65.98724.1721-1.51312.9464-0.98220.52270.1483-0.094-0.02140.2093-0.15860.00750.1271-0.15080.01030.2791-0.14670.0460.28550.0280.1156-61.96430.4246.022
74.9966-2.5385-2.01215.99812.8031.494-0.3335-0.5425-0.12820.17150.4747-0.42770.17720.3197-0.14130.20480.119-0.05730.19060.04730.1603-41.792524.65372.0449
88.0429-0.3771-0.12511.3664-0.41090.3308-0.01530.157-0.6696-0.41820.01970.03590.35650.0355-0.00450.38930.0344-0.0260.0758-0.01030.1649-48.447621.2743-7.5762
910.88693.5482-0.42563.1750.390.16360.10020.13410.2210.2244-0.06040.11920.0808-0.0405-0.03980.2601-0.02-0.03110.13740.07640.2671-58.98817.22660.7412
102.69451.36330.14553.5781-0.08361.5688-0.0340.2114-0.1581-0.08210.1141-0.02490.2684-0.0818-0.08010.12120.0154-0.03510.04610.00220.0794-56.669130.8643-10.6008
115.1055-4.26266.28274.7091-4.21148.68990.01260.2389-0.0206-0.17310.1128-0.1646-0.13750.5208-0.12540.0503-0.01550.03360.2544-0.09230.2308-34.769437.9805-11.0653
128.0745-4.44510.04633.0711.7455.21060.18830.010.1641-0.08070.1134-0.2688-0.00390.3353-0.30170.10810.0273-0.03560.1358-0.03880.2929-34.03440.9506-4.0148
131.18460.05260.43076.2057-0.70671.76390.095-0.25060.09240.12670.02060.107-0.00030.0608-0.11560.0452-0.0179-0.0220.0694-0.03650.0531-46.46146.84812.2747
147.8770.9087-1.42450.5236-0.9131.7760.1886-0.4274-0.0587-0.0218-0.1689-0.0376-0.09510.2904-0.01980.1812-0.0105-0.01220.07860.02690.1382-39.204634.31813.3578
153.9514-1.49282.74650.6144-0.95076.73090.09610.0271-0.1358-0.12680.0195-0.01390.11180.4268-0.11560.2141-0.00180.06460.0949-0.05810.1826-42.288630.2929-12.9004
165.9248-0.38567.71078.93131.71211.6068-0.00010.49460.0135-0.4034-0.287-0.1670.14280.31570.28710.1904-0.01580.02050.1514-0.06320.1702-55.321332.378-19.4708
172.85040.59840.29663.40281.24782.8455-0.08290.25820.0632-0.32530.10440.11260.11290.0717-0.02150.0980.0118-0.0450.03950.00310.0454-59.176437.5492-14.4353
186.94945.9031-2.89046.040.2828.5245-0.1127-0.02560.1068-0.24780.03620.133-0.31420.11380.07650.1610.027-0.04130.12270.00460.1021-59.407343.7932-20.5355
193.63680.65560.96971.67881.11722.22920.07-0.08910.0065-0.0959-0.01260.1143-0.0233-0.0088-0.05740.05280.0072-0.02070.00790.0110.0772-61.686741.5062-6.7818
2012.56333.583-4.00224.9628-4.64174.3852-0.1382-0.0756-0.3798-0.22540.28740.22060.2099-0.2484-0.14920.203-0.0136-0.01530.09090.00590.2458-73.309230.2331-4.6851
212.13145.13210.782412.94420.25284.9039-0.1237-0.0587-0.1225-0.2978-0.0621-0.3571-0.2182-0.20830.18580.13080.0042-0.03470.25730.01340.168-29.121515.7401-37.5653
223.8297-3.6825-0.94516.78295.69648.09990.3330.2465-0.0225-0.3764-0.0963-0.1096-0.5761-0.1717-0.23670.28410.0929-0.03830.31290.01560.2388-37.705726.8039-27.9413
232.20540.0904-0.09671.89671.47564.0136-0.00140.2343-0.0093-0.3943-0.07790.40570.0656-0.33460.07930.14180.0322-0.11940.27510.01130.1589-32.774811.886-29.2946
242.04990.3261-0.5143.76460.54311.4582-0.08040.32850.0367-0.18960.10040.04830.0779-0.2735-0.020.08720.0334-0.04810.18210.00980.0684-25.168114.9071-28.4251
250.15050.9761-1.04096.4804-6.93987.49990.06580.11940.08870.52020.62350.5102-0.6491-0.5462-0.68930.3062-0.0510.13660.4313-0.13960.5038-26.554633.2998-25.8488
261.51280.3220.59493.2854-0.02060.9067-0.09520.20560.0732-0.15170.05750.4079-0.0919-0.32320.03770.0460.033-0.03570.2765-0.01960.179-35.339517.4288-20.5283
276.62120.6137-1.20392.07680.09881.38010.11180.00160.14350.1262-0.04430.2597-0.0623-0.3553-0.06750.05140.0464-0.02260.1347-0.01870.0814-30.127914.8718-13.4951
286.21742.4063-1.97332.0893-0.37010.7605-0.13520.1553-0.1847-0.12820.01590.09180.0186-0.0580.11930.03340.0222-0.04240.14540.00390.0976-26.30229.6798-15.0043
293.3515.1285-2.93369.9383-6.2894.1363-0.0373-0.1321-0.04680.2078-0.0441-0.1484-0.23280.0170.08140.1582-0.00660.01440.1182-0.0620.1359-11.510523.7492-8.4857
304.6350.78753.01963.78331.4796.87760.06410.00330.396-0.2031-0.1098-0.3222-0.41140.22240.04570.25640.02340.03840.06080.01180.2088-11.364734.1721-18.1094
312.8559-0.8483-1.54581.51040.70545.2696-0.0281-0.04-0.0041-0.125-0.0760.0024-0.215-0.17970.10410.0340.0049-0.00260.04080.01690.0689-6.804417.932-23.7578
326.3901-6.38510.38186.4069-0.40110.08840.17880.16940.2065-0.1939-0.1368-0.1476-0.0653-0.0222-0.0420.16010.0167-0.01140.12160.06610.1406-11.662521.268-29.8292
330.7106-0.59130.99370.7212-0.61971.617-0.1630.03350.16890.1042-0.0508-0.1501-0.4022-0.04820.21380.26640.12070.02660.08510.02070.2607-19.809931.4142-20.0041
340.9057-1.7707-0.1515.8746-1.73473.80380.1467-0.10610.15620.21780.34240.4157-0.5145-0.0067-0.48910.18070.07370.12910.1203-0.01640.2772-22.73723.7537-7.1842
355.66951.36451.45034.777-1.75775.60730.0786-0.11720.24290.2648-0.08860.0003-0.167-0.39020.010.08170.05370.01420.1321-0.01880.0891-29.331712.689-4.0188
363.6304-0.9399-2.02671.9135-0.20572.4387-0.0182-0.1863-0.17120.0166-0.086-0.1054-0.0709-0.08080.10420.03810.0248-0.01640.08150.03080.0378-18.4717.4745-11.666
374.812.5827-3.84034.979-3.1796.8159-0.0032-0.1242-0.1773-0.0336-0.1525-0.1220.19090.15370.15560.09140.0367-0.03870.0859-0.01130.0977-13.76257.1047-3.9727
388.0883-0.6666-3.59532.80331.51562.72090.1876-0.28480.19470.45730.0051-0.0672-0.04330.0392-0.19260.13920.02360.01160.12430.030.0619-20.87023.4625-5.7351
391.78010.5820.56351.02080.37280.280.0101-0.1141-0.3991-0.26050.0907-0.2092-0.0837-0.0708-0.10080.0935-0.01160.00790.0911-0.02520.1202-15.32296.575-22.9766
401.1694-1.12612.47776.4477-1.40185.48370.1536-0.1295-0.22260.03030.18210.55430.4162-0.3458-0.33570.1359-0.05210.00590.2494-0.07360.2329-30.6184-2.0092-20.1934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection details
1X-RAY DIFFRACTION1ALL{ AAA|3-8 }
2X-RAY DIFFRACTION2ALL{ AAA|9-16 }
3X-RAY DIFFRACTION3ALL{ AAA|17-21 }
4X-RAY DIFFRACTION4ALL{ AAA|22-26 }
5X-RAY DIFFRACTION5ALL{ AAA|27-46 }
6X-RAY DIFFRACTION6ALL{ AAA|47-60 }
7X-RAY DIFFRACTION7ALL{ AAA|61-73 }
8X-RAY DIFFRACTION8ALL{ AAA|74-83 }
9X-RAY DIFFRACTION9ALL{ AAA|84-93 }
10X-RAY DIFFRACTION10ALL{ AAA|94-135 }
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