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- PDB-7bqa: Crystal structure of ASFV p35 -

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Basic information

Entry
Database: PDB / ID: 7bqa
TitleCrystal structure of ASFV p35
Components60 kDa polyprotein
KeywordsSTRUCTURAL PROTEIN / ASFV / core-shell / p35
Function / homologyviral capsid assembly / virion component / host cell perinuclear region of cytoplasm / 60 kDa polyprotein / Polyprotein pp62
Function and homology information
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.102 Å
AuthorsLi, G.B. / Fu, D. / Chen, C. / Guo, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670731 China
National Natural Science Foundation of China (NSFC)31870733 China
National Natural Science Foundation of China (NSFC)31941011 China
CitationJournal: Protein Cell / Year: 2020
Title: Crystal structure of the African swine fever virus structural protein p35 reveals its role for core shell assembly.
Authors: Li, G. / Fu, D. / Zhang, G. / Zhao, D. / Li, M. / Geng, X. / Sun, D. / Wang, Y. / Chen, C. / Jiao, P. / Cao, L. / Guo, Y. / Rao, Z.
History
DepositionMar 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 60 kDa polyprotein
A: 60 kDa polyprotein


Theoretical massNumber of molelcules
Total (without water)78,0862
Polymers78,0862
Non-polymers00
Water4,648258
1
B: 60 kDa polyprotein


Theoretical massNumber of molelcules
Total (without water)39,0431
Polymers39,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 60 kDa polyprotein


Theoretical massNumber of molelcules
Total (without water)39,0431
Polymers39,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.068, 89.563, 65.080
Angle α, β, γ (deg.)90.000, 89.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 60 kDa polyprotein / CP530R / PCP530R


Mass: 39042.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: CP530R, AFSV47Ss_0139 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0A1E146, UniProt: Q65179*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS pH 6.0, 30% W/V Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.07146 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07146 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.34
ReflectionResolution: 2.1→50 Å / Num. obs: 37964 / % possible obs: 97.8 % / Redundancy: 5.8 % / CC1/2: 0.966 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 1940 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.102→48.723 Å / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 30.66
RfactorNum. reflection% reflection
Rfree0.2276 1827 4.93 %
Rwork0.2004 --
obs0.2033 37034 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.16 Å2 / Biso mean: 26.9837 Å2 / Biso min: 8.38 Å2
Refinement stepCycle: final / Resolution: 2.102→48.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 0 258 4663
Biso mean---36.67 -
Num. residues----536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1035-2.16030.27951140.24752555266985
2.1603-2.22390.28751490.23812632278189
2.2239-2.29560.27881360.22812715285192
2.2956-2.37760.23461340.22782742287693
2.3776-2.47280.29241350.22892806294194
2.4728-2.58520.22471380.2292795293394
2.5852-2.72140.20831560.20942786294293
2.7214-2.89170.24951460.21562758290493
2.8917-3.11470.24471450.20732765291093
3.1147-3.42760.22481270.19662746287392
3.4276-3.92230.20181150.17692677279289
3.9223-4.93680.20121200.1552497261783
4.9368-27.13770.20111570.19622751290890
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.35090.02171.3740.1919-0.18541.0232-0.0185-0.31060.35280.0376-0.05690.0221-0.3112-0.08870.05560.1173-0.00140.00150.2017-0.10690.2665-16.753939.4593-24.8908
25.49674.3281-2.50493.7359-2.10051.23020.0874-0.1548-0.310.1261-0.1707-0.1731-0.02390.02720.07470.18570.02980.02960.2184-0.0610.118-19.368828.7138-18.938
30.619-0.007-0.40530.9357-0.24090.7346-0.0909-0.1480.09590.0644-0.05020.1188-0.0395-0.1799-0.24220.06760.070.04230.3087-0.08440.1452-26.093725.2648-28.2213
40.73810.87320.17471.46040.40060.4690.17870.0083-0.0795-0.0223-0.0806-0.1617-0.06460.2505-0.10440.1391-0.03630.02290.3688-0.11530.1788-29.375432.1226-17.8458
50.3610.03670.02530.48190.33640.9633-0.1433-0.1182-0.15590.2167-0.0226-0.13930.1873-0.2161-0.04550.15010.03160.00110.22670.02030.1396-19.86369.8073-33.1756
60.31730.20290.08771.7161-1.17811.27580.1407-0.3087-0.0991-0.1792-0.19150.04580.21150.0984-0.00870.1357-0.00010.0160.2306-0.0410.1903-29.172910.3598-35.6202
70.76280.1149-0.05370.40980.23140.7999-0.13250.19990.0693-0.07690.1108-0.0589-0.16530.0826-0.05280.02670.03340.02880.2004-0.05340.158-14.241625.2414-38.6549
81.25240.05650.06830.7465-0.22160.80070.0395-0.095-0.19050.1012-0.0582-0.0461-0.0040.16010.01650.05490.02940.00560.13250.00870.1036-44.089518.53827.9866
95.37150.65350.62621.4132-0.03951.9267-0.0337-0.37750.2536-0.04910.1724-0.03640.08060.18570.10890.0661-0.0025-0.15030.235-0.05750.1224-38.882816.500516.7859
100.311-0.0282-0.25130.6987-0.20530.8204-0.0503-0.10040.00560.173-0.02230.0769-0.3990.2678-0.34050.3128-0.0603-0.04450.2357-0.09240.089-43.985436.260813.7153
110.8938-0.1590.51870.7383-0.14751.06360.07980.03970.08270.1096-0.0882-0.0027-0.2590.15310.03490.1374-0.04270.04050.0846-0.01130.1366-44.369939.6809-7.7491
120.11030.13960.06460.42430.06360.48550.11740.1079-0.0416-0.01130.01060.0282-0.1524-0.09780.21030.07940.01890.02430.05990.01950.1262-52.469124.1236-2.3556
130.81470.0346-0.56880.44020.17772.95350.05210.0052-0.0079-0.07250.045-0.04790.089-0.30190.49130.18850.04180.00790.1423-0.13520.1539-56.801511.8645-1.6304
140.8896-0.704-0.04661.5166-0.08570.9487-0.00540.0194-0.0422-0.1732-0.09920.06740.13490.102-0.25780.1570.0180.06580.1214-0.04850.1363-45.156222.8196-13.644
151.28840.12030.40351.07380.09722.06270.0206-0.0181-0.02210.30520.1180.25480.0737-0.21750.20680.11330.03110.01090.05220.01320.1327-53.866632.3357-7.0076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 11 through 32 )B11 - 32
2X-RAY DIFFRACTION2chain 'B' and (resid 33 through 54 )B33 - 54
3X-RAY DIFFRACTION3chain 'B' and (resid 55 through 91 )B55 - 91
4X-RAY DIFFRACTION4chain 'B' and (resid 92 through 109 )B92 - 109
5X-RAY DIFFRACTION5chain 'B' and (resid 110 through 185 )B110 - 185
6X-RAY DIFFRACTION6chain 'B' and (resid 186 through 206 )B186 - 206
7X-RAY DIFFRACTION7chain 'B' and (resid 207 through 298 )B207 - 298
8X-RAY DIFFRACTION8chain 'A' and (resid 11 through 95 )A11 - 95
9X-RAY DIFFRACTION9chain 'A' and (resid 96 through 109 )A96 - 109
10X-RAY DIFFRACTION10chain 'A' and (resid 110 through 145 )A110 - 145
11X-RAY DIFFRACTION11chain 'A' and (resid 146 through 206 )A146 - 206
12X-RAY DIFFRACTION12chain 'A' and (resid 207 through 227 )A207 - 227
13X-RAY DIFFRACTION13chain 'A' and (resid 228 through 245 )A228 - 245
14X-RAY DIFFRACTION14chain 'A' and (resid 246 through 274 )A246 - 274
15X-RAY DIFFRACTION15chain 'A' and (resid 275 through 298 )A275 - 298

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