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- PDB-9mit: Crystal structure of Purine nucleoside phosphorylase from Trichom... -

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Basic information

Entry
Database: PDB / ID: 9mit
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (Hepes bound)
ComponentsPurine nucleoside phosphorylase, putative
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Purine nucleoside phosphorylase / Trichomonas vaginalis
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (Hepes bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase, putative
B: Purine nucleoside phosphorylase, putative
C: Purine nucleoside phosphorylase, putative
D: Purine nucleoside phosphorylase, putative
E: Purine nucleoside phosphorylase, putative
F: Purine nucleoside phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,89014
Polymers159,8616
Non-polymers1,0298
Water23,1671286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22090 Å2
ΔGint-149 kcal/mol
Surface area46460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.816, 49.713, 175.122
Angle α, β, γ (deg.)90.00, 99.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Purine nucleoside phosphorylase, putative


Mass: 26643.428 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_454490 / Plasmid: TrvaA.01033.d.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2EU62
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Index D8: 0.1M HEPES pH 7.5, 25% PEG 3350. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. Hepes acquired from the buffer in 3 of the subunits. plate 14433 well D8 drop 1 , Puck: PSL0911, Cryo: 80% ...Details: Index D8: 0.1M HEPES pH 7.5, 25% PEG 3350. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. Hepes acquired from the buffer in 3 of the subunits. plate 14433 well D8 drop 1 , Puck: PSL0911, Cryo: 80% crystallant + 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 24, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.49→172.88 Å / Num. obs: 234261 / % possible obs: 99.2 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Χ2: 1.09 / Net I/σ(I): 13.9 / Num. measured all: 1617235
Reflection shellResolution: 1.49→1.53 Å / % possible obs: 98.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.923 / Num. measured all: 122232 / Num. unique obs: 17047 / CC1/2: 0.827 / Rpim(I) all: 0.366 / Rrim(I) all: 0.994 / Χ2: 0.84 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIXdev_5533refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→46.49 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1678 11681 4.99 %
Rwork0.1466 --
obs0.1476 234160 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10780 0 66 1286 12132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811342
X-RAY DIFFRACTIONf_angle_d0.97215463
X-RAY DIFFRACTIONf_dihedral_angle_d13.0754235
X-RAY DIFFRACTIONf_chiral_restr0.0791796
X-RAY DIFFRACTIONf_plane_restr0.0081995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.25453860.23977251X-RAY DIFFRACTION97
1.51-1.520.24653550.22977399X-RAY DIFFRACTION99
1.52-1.540.24573810.22387212X-RAY DIFFRACTION98
1.54-1.560.25263860.21487268X-RAY DIFFRACTION98
1.56-1.580.24684210.21157362X-RAY DIFFRACTION99
1.58-1.610.25613850.22517210X-RAY DIFFRACTION97
1.61-1.630.23334180.23667321X-RAY DIFFRACTION99
1.63-1.650.27274060.25197325X-RAY DIFFRACTION98
1.65-1.680.28923660.22367343X-RAY DIFFRACTION99
1.68-1.710.22553700.1977375X-RAY DIFFRACTION99
1.71-1.740.21834020.18597370X-RAY DIFFRACTION99
1.74-1.770.23610.17597442X-RAY DIFFRACTION99
1.77-1.80.20323730.16767292X-RAY DIFFRACTION99
1.8-1.840.19444120.15937402X-RAY DIFFRACTION99
1.84-1.880.18563900.14817374X-RAY DIFFRACTION100
1.88-1.920.17123760.14667399X-RAY DIFFRACTION99
1.92-1.970.18023740.15477445X-RAY DIFFRACTION100
1.97-2.020.17964110.16127372X-RAY DIFFRACTION99
2.02-2.080.18733920.15917418X-RAY DIFFRACTION99
2.08-2.150.16453790.13927468X-RAY DIFFRACTION100
2.15-2.230.15933990.1337419X-RAY DIFFRACTION100
2.23-2.310.16534110.13347456X-RAY DIFFRACTION100
2.31-2.420.15214000.13137472X-RAY DIFFRACTION100
2.42-2.550.15083550.12817522X-RAY DIFFRACTION100
2.55-2.710.14883940.12697507X-RAY DIFFRACTION100
2.71-2.920.16064040.13737543X-RAY DIFFRACTION100
2.92-3.210.14883730.13377512X-RAY DIFFRACTION100
3.21-3.670.15144280.13347543X-RAY DIFFRACTION100
3.67-4.630.1284020.11677607X-RAY DIFFRACTION100
4.63-46.490.16123710.157850X-RAY DIFFRACTION100
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)
14.0586-0.095-0.65721.13840.05751.99070.0096-0.25680.11570.1887-0.0222-0.1149-0.12980.24330.01410.2334-0.0509-0.03630.1785-0.00470.1364-21.369932.779674.1556
21.06930.19290.13060.45150.11241.04310.02430.0269-0.06550.0864-0.0332-0.05780.03150.08940.00640.1375-0.0095-0.00540.10360.01850.1239-24.883721.927657.8628
33.13891.04830.23846.1492-1.05152.48060.1443-0.2556-0.28860.4701-0.1442-0.33110.13950.16490.01550.25-0.023-0.05960.25990.03380.1887-12.992319.030868.2515
46.52461.529-5.24312.4675-1.3764.2687-0.1781-0.6362-0.80790.154-0.2283-0.1180.39220.46110.38740.25940.0060.01140.20390.05650.1976-39.215911.847479.6309
52.65620.2058-1.64760.4765-0.1012.17090.0187-0.25220.05440.1349-0.03260.0088-0.09860.137-0.0160.2578-0.01460.00730.18020.00910.151-42.98223.866884.5876
60.75940.0386-0.16030.3944-0.09521.22250.03350.0185-0.0130.0611-0.01690.0249-0.0792-0.0368-0.0180.1651-0.00090.03040.10350.00930.1352-48.745923.921567.5363
72.9738-0.5428-1.57955.30535.52069.32180.03350.0992-0.10170.3374-0.33570.48160.1754-0.65720.25910.21770.0020.06240.22760.00550.1943-63.596626.110576.0798
82.0847-0.2488-0.41040.290.37060.95830.0190.13260.10270.1131-0.00610.0567-0.1421-0.0922-0.06660.21130.02520.02810.09940.01650.1509-49.616535.454164.3556
90.996-0.1371-0.29280.10650.13881.4810.0483-0.0010.14280.07860.00860.0273-0.2927-0.0137-0.03570.1920.00580.03170.11190.00420.1418-50.846132.237965.1992
103.08443.3672-1.37419.5861-2.21063.77350.198-0.26890.09710.2806-0.1755-0.0903-0.24710.2063-0.00690.22120.01280.03390.1868-0.0190.1434-53.366333.555581.7413
112.9105-0.26690.33450.5807-0.14860.63670.02270.3834-0.1152-0.0866-0.0471-0.21070.12460.54260.02320.16690.05670.00960.4237-0.0090.1852-12.674615.779522.8379
121.3733-0.14080.0141.5433-0.02381.29030.05870.105-0.00380.0849-0.0472-0.09220.00790.2652-0.03780.11590.0040.00040.22810.02060.1074-18.835921.895532.1944
132.77910.7612-0.90481.2332-0.41951.5910.0346-0.0065-0.02770.0356-0.0703-0.08130.00640.23970.02390.1160.001-0.01520.15960.00830.0987-22.483422.477142.599
141.5487-0.0096-0.43430.48550.11881.1908-0.02550.00190.1101-0.0359-0.0104-0.047-0.33110.08240.02940.186-0.0353-0.00620.17970.03010.1567-25.645133.75836.2462
151.2975-0.2724-0.19650.45360.24621.57690.04990.13340.1787-0.0212-0.0394-0.0429-0.22160.1207-0.00010.1691-0.0256-0.00660.19850.03350.1668-23.433830.65437.7092
163.9131-2.9861.12963.8371-3.15274.3690.26640.61320.527-0.2279-0.4642-0.4581-0.24440.4940.2630.2292-0.0269-0.00290.48190.11710.312-7.945630.060430.8355
170.8615-0.15320.49580.78130.0662.46510.03230.26110.0471-0.1513-0.0569-0.0507-0.1110.16920.02340.16290.01340.00950.30320.03370.1331-31.615226.553210.3541
180.87271.5932-0.10786.5235-0.7291.56170.06710.1034-0.02540.0265-0.05110.2330.1566-0.1507-0.04160.16970.0092-0.00030.315-0.02080.1713-42.396315.893415.6586
190.58-0.3557-0.53551.07770.68671.65040.01960.02830.00310.0346-0.0214-0.0193-0.0102-0.1056-0.00060.150.0009-0.01130.2640.00460.1455-46.355223.774127.9531
202.92030.69491.07437.02661.09411.71260.07980.1596-0.0627-0.2288-0.42220.523-0.2005-0.68650.38140.16020.0385-0.03040.4165-0.05810.1545-52.356519.42547.873
211.1514-0.24580.46060.46130.40551.8269-0.00760.0775-0.1546-0.051-0.02860.00860.1757-0.1968-0.02080.1561-0.02690.00310.2081-0.02440.1327-42.399910.950123.4911
220.67810.17850.08241.2630.12490.74050.02750.0611-0.03650.0693-0.04340.03650.0493-0.12440.01960.1625-0.0085-0.00650.2701-0.01770.1445-45.122918.333224.8195
231.2698-0.6501-0.79862.42891.91362.31690.00890.0344-0.15490.0301-0.0824-0.05560.57140.07550.06130.2350.0007-0.02740.2943-0.02240.168-41.18827.372218.1543
242.6274-3.27832.23648.788-5.22315.580.16250.19130.011-0.3008-0.2056-0.17380.27810.02310.02330.16910.0127-0.0090.3537-0.04880.1557-40.864112.73255.5989
251.3397-0.51530.53631.74530.18832.4453-0.02040.42720.4265-0.08520.01630.2552-0.4206-0.43990.0180.20240.09950.02890.52190.11990.3797-79.251134.318844.9207
263.06650.2732-1.11541.3602-0.6923.07320.09570.1872-0.03730.1073-0.04250.38220.0045-0.52110.07350.16610.00580.04490.60890.06530.3543-87.573924.182750.6834
271.4571-0.075-0.00190.890.03030.0052-0.02120.270.1280.04790.03670.2385-0.0868-0.4512-0.03370.15770.05920.02580.43490.04530.2561-77.584628.951148.6824
282.653-0.9974-0.01093.0639-0.80581.7969-0.0774-0.0414-0.26530.17450.07060.2060.0851-0.2482-0.03170.1342-0.01910.03020.27810.01110.2105-70.928318.501756.8948
292.06090.1712-0.09860.86360.05950.8944-0.01670.12640.0027-0.04780.01240.0844-0.008-0.0946-0.03010.17060.02250.02230.18350.01050.163-57.827625.735952.8877
309.42795.4546-3.10265.6011-2.17484.0160.1168-0.5389-0.07560.4939-0.11840.2266-0.153-0.1488-0.00860.20740.02720.0730.35710.01290.232-72.520123.582968.8356
312.42120.1027-0.66160.65830.05351.728-0.05190.0639-0.24350.04460.10210.15570.198-0.11430.11360.1751-0.0190.03290.20920.00790.2364-64.966212.808154.2956
321.9895-0.1164-0.12230.901-0.12211.1943-0.02380.1462-0.07210.01460.05910.10530.0238-0.1909-0.00680.156-0.00420.02490.21410.0020.1618-61.615220.385254.4797
332.86920.5725-0.08011.9562-0.35221.7158-0.0910.1558-0.6967-0.0355-0.120.29670.3382-0.30730.06530.2274-0.04370.06290.2766-0.01410.3438-69.78349.718555.7596
342.96560.0427-0.28328.58242.14782.5867-0.02050.1486-0.43540.1447-0.08280.42630.266-0.51410.05870.211-0.03310.06070.41860.00380.3674-80.711316.261360.5399
350.6574-0.03480.37060.04070.10350.5943-0.01610.1741-0.332-0.07490.05510.08820.2039-0.2680.01530.2622-0.23990.00120.7139-0.04550.3821-76.48596.665432.1951
360.78170.0341-0.07210.2124-0.00640.00590.0260.40670.0492-0.1413-0.01020.1959-0.0769-0.40650.03220.1926-0.029-0.01370.86660.060.3146-79.104221.684925.7746
370.00690.0121-0.04910.0339-0.14090.529-0.03580.3231-0.1038-0.10650.12730.1680.1019-0.23460.03940.1711-0.1736-0.05530.9707-0.00780.3403-82.045714.339825.8647
381.28740.28410.30970.65020.29070.6203-0.08120.48650.0144-0.14710.1130.07330.0519-0.49680.03170.1821-0.05060.00920.594-0.00150.2267-68.277420.449327.7172
391.4416-0.10231.4671.0609-0.02771.6644-0.01160.29290.04020.0237-0.03270.10670.0052-0.21990.0260.127-0.02540.01450.3245-0.00750.1445-54.471120.004431.6957
404.2402-1.5323.29742.2699-1.23873.6842-0.01380.47210.1131-0.2197-0.03940.0878-0.04150.09990.07660.1964-0.0573-0.0530.81740.0110.1791-64.196521.485311.8919
410.4674-0.37480.75691.0676-0.45351.30270.0230.38520.20740.00350.0980.158-0.1514-0.25970.0050.12710.02610.00010.42670.07780.2053-60.878732.453329.8362
421.08670.3962-0.62461.3548-0.53681.0305-0.03290.29580.0189-0.00770.10760.0861-0.0183-0.3966-0.07110.13820.009-0.0180.36180.00970.1465-57.531125.232829.0506
432.4786-0.28890.90580.5368-0.84811.4232-0.07920.33960.4579-0.14340.00140.4639-0.298-0.49690.09020.21370.08540.01970.62730.09870.3218-66.131334.759825.2964
443.1291-0.4480.12581.7810.17320.5078-0.07620.05850.1849-0.01590.30760.1652-0.0656-0.41890.07470.2030.0215-0.02520.93980.09750.3056-74.569327.437217.3898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 214 )
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 236 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 15 )
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 55 )
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 131 )
7X-RAY DIFFRACTION7chain 'B' and (resid 132 through 144 )
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 166 )
9X-RAY DIFFRACTION9chain 'B' and (resid 167 through 214 )
10X-RAY DIFFRACTION10chain 'B' and (resid 215 through 236 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 55 )
12X-RAY DIFFRACTION12chain 'C' and (resid 56 through 103 )
13X-RAY DIFFRACTION13chain 'C' and (resid 104 through 145 )
14X-RAY DIFFRACTION14chain 'C' and (resid 146 through 166 )
15X-RAY DIFFRACTION15chain 'C' and (resid 167 through 214 )
16X-RAY DIFFRACTION16chain 'C' and (resid 215 through 236 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 79 )
18X-RAY DIFFRACTION18chain 'D' and (resid 80 through 103 )
19X-RAY DIFFRACTION19chain 'D' and (resid 104 through 131 )
20X-RAY DIFFRACTION20chain 'D' and (resid 132 through 144 )
21X-RAY DIFFRACTION21chain 'D' and (resid 145 through 166 )
22X-RAY DIFFRACTION22chain 'D' and (resid 167 through 195 )
23X-RAY DIFFRACTION23chain 'D' and (resid 196 through 214 )
24X-RAY DIFFRACTION24chain 'D' and (resid 215 through 236 )
25X-RAY DIFFRACTION25chain 'E' and (resid -2 through 22 )
26X-RAY DIFFRACTION26chain 'E' and (resid 23 through 41 )
27X-RAY DIFFRACTION27chain 'E' and (resid 42 through 79 )
28X-RAY DIFFRACTION28chain 'E' and (resid 80 through 103 )
29X-RAY DIFFRACTION29chain 'E' and (resid 104 through 131 )
30X-RAY DIFFRACTION30chain 'E' and (resid 132 through 144 )
31X-RAY DIFFRACTION31chain 'E' and (resid 145 through 166 )
32X-RAY DIFFRACTION32chain 'E' and (resid 167 through 195 )
33X-RAY DIFFRACTION33chain 'E' and (resid 196 through 214 )
34X-RAY DIFFRACTION34chain 'E' and (resid 215 through 236 )
35X-RAY DIFFRACTION35chain 'F' and (resid 2 through 15 )
36X-RAY DIFFRACTION36chain 'F' and (resid 16 through 33 )
37X-RAY DIFFRACTION37chain 'F' and (resid 34 through 55 )
38X-RAY DIFFRACTION38chain 'F' and (resid 56 through 103 )
39X-RAY DIFFRACTION39chain 'F' and (resid 104 through 131 )
40X-RAY DIFFRACTION40chain 'F' and (resid 132 through 145 )
41X-RAY DIFFRACTION41chain 'F' and (resid 146 through 166 )
42X-RAY DIFFRACTION42chain 'F' and (resid 167 through 195 )
43X-RAY DIFFRACTION43chain 'F' and (resid 196 through 214 )
44X-RAY DIFFRACTION44chain 'F' and (resid 215 through 236 )

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