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- PDB-8zwq: pseudorabies virus dUTPase structure -

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Basic information

Entry
Database: PDB / ID: 8zwq
Titlepseudorabies virus dUTPase structure
ComponentsdUTPase
KeywordsVIRAL PROTEIN / Pseudorabies virus / DUTPase / Dimer
Function / homologyDeoxyuridine 5'-triphosphate nucleotidohydrolase / dUTP metabolic process / dUTPase-like / dUTPase / dUTP diphosphatase activity / dUTPase, trimeric / dUTPase-like superfamily / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / dUTPase
Function and homology information
Biological speciesSuid alphaherpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsWang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81801998 China
CitationJournal: To Be Published
Title: Structural definition of pseudorabies virus dUTPase reveals a novel folding dimer in the herpesviruses family
Authors: Wang, Y.
History
DepositionJun 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dUTPase
C: dUTPase
B: dUTPase
D: dUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2156
Polymers118,8834
Non-polymers3322
Water5,855325
1
A: dUTPase
C: dUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7744
Polymers59,4412
Non-polymers3322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dUTPase
D: dUTPase


Theoretical massNumber of molelcules
Total (without water)59,4412
Polymers59,4412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.249, 103.264, 98.733
Angle α, β, γ (deg.)90.000, 99.472, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
dUTPase


Mass: 29720.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid alphaherpesvirus 1 / Gene: UL50
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: G3G945
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.1 M Tris/HCl (pH 8.5) 2.0 M Ammonium hydrogenphosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.0083 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0083 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 46889 / % possible obs: 98.97 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.54 Å2 / CC1/2: 0.87 / Net I/σ(I): 12.4
Reflection shellResolution: 2.23→2.28 Å / Rmerge(I) obs: 0.519 / Num. unique obs: 4491 / CC1/2: 0.87 / Rpim(I) all: 0.283 / Rrim(I) all: 0.653

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→48.45 Å / SU ML: 0.385 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 42.8809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3385 2340 5.01 %
Rwork0.2771 44331 -
obs0.2802 46671 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.36 Å2
Refinement stepCycle: LAST / Resolution: 2.23→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6868 0 21 325 7214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097101
X-RAY DIFFRACTIONf_angle_d1.14779711
X-RAY DIFFRACTIONf_chiral_restr0.0831051
X-RAY DIFFRACTIONf_plane_restr0.00831289
X-RAY DIFFRACTIONf_dihedral_angle_d16.00822621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.280.4371130.34442438X-RAY DIFFRACTION93
2.28-2.330.39861460.32562605X-RAY DIFFRACTION99.67
2.33-2.380.36721250.30612651X-RAY DIFFRACTION99.75
2.38-2.440.39191440.29712596X-RAY DIFFRACTION99.67
2.44-2.510.34211350.29372614X-RAY DIFFRACTION99.71
2.51-2.580.38071420.2812614X-RAY DIFFRACTION99.78
2.58-2.670.36191290.28962628X-RAY DIFFRACTION99.42
2.67-2.760.37361330.27732605X-RAY DIFFRACTION99.53
2.76-2.870.30671460.26442613X-RAY DIFFRACTION99.57
2.87-30.34241380.2742616X-RAY DIFFRACTION99.46
3-3.160.36161450.27192603X-RAY DIFFRACTION99.64
3.16-3.360.32791510.27042615X-RAY DIFFRACTION99.28
3.36-3.620.31991460.26082590X-RAY DIFFRACTION99.45
3.62-3.980.34591380.25322672X-RAY DIFFRACTION99.79
3.98-4.560.27261360.24352623X-RAY DIFFRACTION99.5
4.56-5.740.32691360.26462650X-RAY DIFFRACTION99.57
5.74-48.450.34221370.31652598X-RAY DIFFRACTION96.07
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)
10.03362472344940.008061937610650.02626160433890.065160359827-0.01496850240690.0228904802941-0.01372699741130.0708020081130.170836245090.1859636095650.0588525589917-0.07987614823230.0202378926575-0.124381306037-4.89666377285E-50.232398531301-0.027023955501-0.02367968704670.2326600520670.02338093458680.20193699641712.527706148-11.38548262515.8711845609
20.005872653090.00199656173910.007215299357860.004302302978850.003242124034080.006765420439233.67121874807E-5-0.03501812421270.07234777757540.0903160248264-0.002494574643620.00849887604394-0.06235312392250.0203915245949-0.007204300614030.1765303753230.09626047422740.0469484576420.1672555378390.1570994451270.0005894741738076.43815138799-9.1043915644617.7136830837
30.05031142312760.03668261701240.04004161779710.1369732576060.02417173140980.114958681571-0.0159171026570.1003212374040.06045619748270.1551059594460.0447431812266-0.1713075450280.1624995222560.2095764936640.02731541325010.2156178363920.02556902510780.04554154957740.18785796880.04790624977830.25853974952618.2821490149.083249525133.82236225408
40.0663058265909-0.01877870867010.008442465683210.00422222929856-0.003130260787860.002035977741980.1224128058850.05444068825220.1794993585280.0935850884928-0.04427530398720.244782522368-0.1560252304530.04163792577960.01741036930660.3138931571860.004120970157220.07609149564550.1651707139590.08242875874870.2948892026997.4272466956412.67517294916.8107346181
50.01757562840190.0277956056021-0.004707912929450.0275720398708-0.001436318621670.000149983971773-0.0944146099142-0.1195156828340.05990468760340.0577209469587-0.0220150272228-0.100315671895-0.0309198447138-0.0235684504232-0.0724100718779-0.0371619667822-0.0212391555871-0.1298450797560.2040967628280.07437566440590.10502501795710.76785646213.9626161635214.191922709
60.01416309085540.0340657920146-0.02040251817820.04490057014450.009870756061410.1493776381630.03544061794250.1354805432780.0684540128244-0.0184609872783-0.06364646720130.0395871640578-0.0540152530524-0.0769952802003-0.01007244851720.1231415570370.0384048588839-0.06624691718880.2383925942190.08395478411360.3298026191674.793021274989.519473352712.6916986282
70.01117935383460.00111709569384-0.02737085865870.2267005486030.007801125675610.0378580856830.0286432436529-0.0105134504730.0667824065017-0.102310293672-0.1546358304920.129490674684-0.0714674961766-0.0463732248121-0.03361748778870.117807957873-0.028551530863-0.02211047424520.176860754516-0.00313728107350.1438336701017.35502699362.251658238779.72809722357
80.03976600931240.04977049167570.009366358497180.05637817559440.01049020292670.001764635885420.113953198509-0.08443528927190.03067156335820.0558982712325-0.0358966000208-0.00129574698023-0.04483490184380.03854113570910.009489987299820.255914997339-0.04042647326770.07735398896690.352438806021-0.140520198830.20994616189212.5459005462-17.57557234683.70901241071
90.02884410249820.08867937576250.004473094153550.2360129513550.0002988056529580.06176555001020.0551669118424-0.008999463748510.04559359717430.0528104324461-0.03247678189150.183507801729-0.0433584234883-0.1263113804280.002180304302920.2058978425540.0422800756947-0.006134801287540.2293965230980.02127113184970.1964410510016.25704793352-36.06521198910.9152217325
100.098255590631-0.0163357653240.03654274717070.04555832825860.07917132520010.1866919807426.26877021043E-50.0578214740105-0.1440894182020.07888639241730.03429677848180.04953288683710.1145460099670.1369304779050.06404803362210.241799816190.04577507990690.02113412113310.093023878851-0.01859423375230.2475850737517.4388509844-57.76633929.89732183638
110.423250031987-0.324860459729-0.1980720195990.6483990493190.1788426179670.506578644091-0.13557976490.0395224281549-0.1459617084350.172785266637-0.1384562839930.09715267964510.1586738864930.120481967799-0.8686056950850.2777801555730.000754484294795-0.04410206590454.57050134559E-50.004026520460610.07464308545649.93292106996-51.912532939915.1706352367
120.0696809713841-0.0323433314268-0.04330234612750.0356224092081-0.008919877106650.0659523416501-0.1571355332960.0177802883246-0.0318956734879-0.0317847107199-0.03828844897520.0398556713961-0.005434733479790.00588997390831-0.04425077698280.283138470192-0.0828650502985-0.06227389067440.234486587596-0.03852237791490.34119345665319.2457856438-29.93489283711.922228171
130.168887576994-0.1204289428260.1114998694270.266174342836-0.1080058950220.08041027621190.0598102487690.06357953040540.19799068706-0.0142110018662-0.121573918793-0.06241532898130.05230137170750.131779490334-0.07261432382680.1838807936280.0126637876434-0.005046310925360.189077478542-0.006712033590930.11787759986529.5416446606-4.6830571185131.6260044341
140.1478314228590.0547004793184-0.1122182946730.049160943528-0.0879253760680.178468725536-0.0369423641942-0.04481318043720.08894980546920.0691889860689-0.170839597843-0.167620209034-0.005724057365770.0964524442736-0.4177973750240.03595166131850.03942997250270.01866594079870.290937922427-0.1382804928550.19333867927827.9127140046.623522521545.4640107132
150.1554610565940.02249923222230.1650063189740.00919855853560.0394341786990.202932340623-0.00765102042475-0.1183372098480.0909596450909-0.231612017062-0.0585543981037-0.0433101457872-0.200911750542-0.100616253967-0.005476053719450.2344249032350.04699343992250.0777496521550.134076428741-0.02422645658880.4057474123524.899498038816.601362324837.1919695367
160.1246701688320.01662255585290.09333378755620.0389510070544-0.001368685397540.08213295611990.0182325995454-0.130737321620.192458788313-0.06968921453690.114964875216-0.107916610434-0.0538384371179-0.02536282809690.08089692139970.256690094344-0.1171941747450.04527247409270.205908792293-0.1224352276990.38657327887632.170176491914.708295906646.0041442386
170.0374211453305-0.05237180571320.01420838772650.0748742275467-0.04904354339880.04249788454480.06657473789730.1233309378160.438866802826-0.116931594210.0296289280903-0.1209248285830.02750292302190.08335680014725.27676357979E-60.198590626064-0.02690411916180.02616510715180.218235868093-0.01899093369360.4324226115133.920412187714.143129927435.8724366584
180.1681073565570.263561903482-0.05911015678250.44877821898-0.05885086567630.01468158545720.208922994085-0.06134018703040.155016024940.101691909481-0.1644958361160.0224689898215-0.08842542809010.01249472173130.005041690382890.1945819953950.0516823654820.03117391064530.178615038848-0.0224870847320.3065869510731.617557149912.372170361136.5081869016
190.1393159494460.09135955371870.05180137002350.0747520138007-0.01172130730210.111738099530.0716798268064-0.1649015298640.183289143415-0.01565643709770.0698359238144-0.08513834025920.007765842534870.001101442311170.1465114144530.0648712693909-0.02580160048880.03561267763190.2543541126230.03963994002720.39946544393933.9761899995-6.0967498597741.4543152478
200.001935474091390.00343423879516-0.008473356689210.0736456939608-0.001432854890050.02357832397510.0874620344713-0.08487802212170.01095149380150.002347773669820.0640786637520.299047604742-0.0565452805498-0.02133415125970.001329661619240.2430098671190.04660341200610.07814839450740.1722677568930.01755630247730.21963875157830.4313696186-21.268025744240.1966279953
210.00590044378483-0.007297075299140.003027136813230.01208077105190.01255958638530.0605361435353-0.0388738480968-0.00351289138385-0.0668195265715-0.04835941871450.0724641669063-0.134085382352-0.03937160570390.09667449836850.0001323032819240.113160239221-0.02822642855390.06589940373480.1925816746150.02964648625250.30412896152241.4017231825-29.791465230134.2595201542
220.0571243664703-0.04903725663630.01734925174890.133684651776-0.01718595354990.01104489659120.0623713393099-0.0556806311768-0.08057267749-0.1069888011830.129943803128-0.1250999592440.00754197235994-0.007597289305880.05158430755640.193102832437-0.01630429817120.009527575311720.2137421258130.002325957613320.16748043304835.1806764359-32.602711446138.7781391146
23-0.0012866572449-0.004545009101310.01519773107620.01368066667810.01737701641680.069299823463-0.0627178395357-0.03982144752490.08312282143170.02946947332270.1109822082010.0725095071115-0.0633135715547-0.06853997612420.004179973760250.177874893834-0.06272679426820.01856796391480.1933025816730.01159753298380.23954524307721.6589912582-41.450455541137.64217716
240.01575112029080.0214120550683-0.01737278094980.0212211025049-0.02229252579330.01963769685730.0388711884849-0.143292467704-0.13080380981-0.08801055825780.0141909684162-0.1384141763870.212073494129-0.135621517534-1.67471216772E-60.3323835515540.01943391726390.04700043172830.233134895127-0.0176629623520.25303779009125.368208199-49.577755322444.2643581614
251.98494422386E-5-0.001791433624830.001457154097240.0142946859325-0.07426043547790.227792585848-0.04531246362060.0185143663206-0.0480742389102-0.26813094056-0.004413684979790.00677956445510.292713852368-0.0609730940377-0.01998497969660.245980235695-0.03410590732510.02929063909130.138818039971-0.006288595715110.28922255905126.3799596768-53.854556908232.6737315088
260.460025869586-0.07379860888920.0553479634360.0136425619095-0.02357732838110.33500270746-0.037449604428-0.0778334138268-0.001749572928880.00559547832351-0.01010413865480.04061475935750.07131756592860.192018044941-0.05569556351510.159223700322-0.0302176040132-0.246133461790.1583642540680.0901630565007-0.029598615627232.9285196458-44.83908314637.1274847299
270.0123729746823-0.0412795571080.004112399406870.152768293481-0.03579780323420.005832279288390.04300203603270.0188466566374-0.0154337782571-0.1841625386670.013360291263-0.1691864026730.3124618898720.0297135874544-0.00158441339650.260341049054-0.0337937778804-0.03305558962980.158025381393-0.02037811084640.12399329902332.4961025395-50.449550377831.1279961919
280.1636398526540.006582886338730.01693220014430.232891459789-0.03337122233930.01892487301180.0627966304251-0.0670006204131-0.03662942709610.1043279346770.102452415609-0.004678540072880.240288326911-0.02288682650940.1358315219650.2043062894670.0301036052426-0.06766903950390.1978886953970.08908231198720.22945129527928.0850506106-46.246735726635.5575791061
290.0200977328860.0193881853290.01397611222810.02552877162670.01783717324610.01217567870840.0079248449750.0576730372432-0.0794246642937-0.008781371845760.0297211494387-0.0614878914019-0.0144211801808-0.09127096621950.006698280069390.297005131070.05177520850940.03365577636410.3143884826460.08422646907770.21741720592631.88667508-34.545666054126.5491595314
300.0180356870755-0.00916857416169-0.005165053809080.0271350974102-0.0172276445730.0187602621229-0.0597801193812-0.000875454742475-0.0228175484039-0.0123204212914-0.0562726057276-0.04534801515710.01440110295520.0526316668937-0.07632098888210.2079243034120.1973138810740.08001807127080.2933083336380.1097399647360.27492338388322.0026839252-23.636745671936.9406221496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 111 )
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 165 )
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 182 )
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 238 )
8X-RAY DIFFRACTION8chain 'A' and (resid 239 through 248 )
9X-RAY DIFFRACTION9chain 'C' and (resid 25 through 111 )
10X-RAY DIFFRACTION10chain 'C' and (resid 112 through 165 )
11X-RAY DIFFRACTION11chain 'C' and (resid 166 through 238 )
12X-RAY DIFFRACTION12chain 'C' and (resid 239 through 248 )
13X-RAY DIFFRACTION13chain 'B' and (resid 25 through 102 )
14X-RAY DIFFRACTION14chain 'B' and (resid 103 through 124 )
15X-RAY DIFFRACTION15chain 'B' and (resid 125 through 150 )
16X-RAY DIFFRACTION16chain 'B' and (resid 151 through 172 )
17X-RAY DIFFRACTION17chain 'B' and (resid 173 through 198 )
18X-RAY DIFFRACTION18chain 'B' and (resid 199 through 228 )
19X-RAY DIFFRACTION19chain 'B' and (resid 229 through 248 )
20X-RAY DIFFRACTION20chain 'D' and (resid 25 through 39 )
21X-RAY DIFFRACTION21chain 'D' and (resid 40 through 52 )
22X-RAY DIFFRACTION22chain 'D' and (resid 53 through 102 )
23X-RAY DIFFRACTION23chain 'D' and (resid 103 through 124 )
24X-RAY DIFFRACTION24chain 'D' and (resid 125 through 143 )
25X-RAY DIFFRACTION25chain 'D' and (resid 144 through 165 )
26X-RAY DIFFRACTION26chain 'D' and (resid 166 through 182 )
27X-RAY DIFFRACTION27chain 'D' and (resid 183 through 203 )
28X-RAY DIFFRACTION28chain 'D' and (resid 204 through 228 )
29X-RAY DIFFRACTION29chain 'D' and (resid 229 through 238 )
30X-RAY DIFFRACTION30chain 'D' and (resid 239 through 248 )

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