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- PDB-8cyl: Ast89 P domain -

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Basic information

Entry
Database: PDB / ID: 8cyl
TitleAst89 P domain
Components(Capsid protein VP60) x 2
KeywordsVIRAL PROTEIN / RHDV
Function / homology
Function and homology information


calicivirin / host cell endoplasmic reticulum / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity ...calicivirin / host cell endoplasmic reticulum / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding
Similarity search - Function
: / Viral genome-linked protein / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. ...: / Viral genome-linked protein / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesLagovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.888 Å
AuthorsLeuthold, M. / Kilic, T. / Hansman, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: J.Virol. / Year: 2022
Title: Structural Basis for Rabbit Hemorrhagic Disease Virus Antibody Specificity.
Authors: Leuthold, M.M. / Kilic, T. / Devant, J.M. / Landeta, O. / Parra, F. / Dalton, K.P. / Hansman, G.S.
History
DepositionMay 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP60
B: Capsid protein VP60


Theoretical massNumber of molelcules
Total (without water)69,5952
Polymers69,5952
Non-polymers00
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-20 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.590, 78.410, 100.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Capsid protein VP60


Mass: 35106.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lagovirus / Strain: AST89 / Gene: ORF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86119
#2: Protein Capsid protein VP60


Mass: 34488.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lagovirus / Strain: AST89 / Gene: ORF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86119
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid (pH 4) and 30% PEG6000

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.888→42.4255 Å / Num. obs: 47320 / % possible obs: 98.2 % / Redundancy: 1.36 % / Biso Wilson estimate: 19.25 Å2 / CC1/2: 0.903 / Net I/σ(I): 9.19
Reflection shellResolution: 1.888→42.4255 Å / Num. unique obs: 47320 / CC1/2: 0.903

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X1W

4x1w


Resolution: 1.888→42.415 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1949 2366 5 %
Rwork0.1628 --
obs0.1644 47320 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.888→42.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 0 445 5298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045034
X-RAY DIFFRACTIONf_angle_d0.776939
X-RAY DIFFRACTIONf_dihedral_angle_d2.5823856
X-RAY DIFFRACTIONf_chiral_restr0.051786
X-RAY DIFFRACTIONf_plane_restr0.005925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8884-1.92690.2321330.21252515X-RAY DIFFRACTION95
1.9269-1.96880.25891380.20462631X-RAY DIFFRACTION99
1.9688-2.01460.23621360.18742580X-RAY DIFFRACTION98
2.0146-2.0650.23331350.17672568X-RAY DIFFRACTION96
2.065-2.12080.21441400.17112650X-RAY DIFFRACTION99
2.1208-2.18320.22991380.16952629X-RAY DIFFRACTION99
2.1832-2.25370.23791390.17122640X-RAY DIFFRACTION99
2.2537-2.33430.2131390.17312643X-RAY DIFFRACTION99
2.3343-2.42770.20981380.16942620X-RAY DIFFRACTION99
2.4277-2.53820.20491390.1742646X-RAY DIFFRACTION99
2.5382-2.6720.20831370.17192607X-RAY DIFFRACTION97
2.672-2.83940.20741420.17592684X-RAY DIFFRACTION100
2.8394-3.05850.19451410.17742680X-RAY DIFFRACTION99
3.0585-3.36620.19531410.17132681X-RAY DIFFRACTION99
3.3662-3.8530.18751380.15112618X-RAY DIFFRACTION96
3.853-4.85330.14861440.12532736X-RAY DIFFRACTION99
4.8533-42.4150.14811480.14142826X-RAY DIFFRACTION98
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)
10.0477-0.1694-0.17441.64561.73681.9688-0.0023-0.10110.3692-0.01580.12690.2197-0.26410.0646-0.10250.21240.00050.03320.2338-0.0090.2879-8.6975-1.812526.5285
21.73740.9739-0.82261.8919-0.61221.336-0.0324-0.03950.0686-0.00280.0495-0.0502-0.0297-0.0337-0.02220.1470.0302-0.010.1504-0.00040.14114.3282-5.194712.8931
31.03821.10090.81811.43630.57281.81190.03850.03910.1312-0.03390.1131-0.2116-0.15950.129-0.17390.10920.0023-0.00050.09110.04080.202118.79420.313-3.4458
40.5146-0.39580.43321.2399-0.78621.973-0.01790.06950.0406-0.0321-0.0215-0.1510.03490.10690.04880.1193-0.00680.01560.1417-0.00160.197616.0365-7.2985-3.247
50.55470.2311-0.10761.07380.00620.9154-0.02080.04590.0599-0.07140.0543-0.2244-0.08420.148-0.04510.12960.00570.0090.15450.0190.204419.4878-4.8804-4.0622
61.04680.0306-0.360.6954-0.27280.8461-0.008-0.1357-0.05560.06610.0145-0.0521-0.02370.0451-0.00060.14310.0175-0.00530.15030.01280.15447.5181-14.35689.2142
71.7391-0.1284-0.22681.70460.8111.58970.002-0.25880.1410.10170.0555-0.1184-0.0851-0.0234-0.05150.1475-0.004-0.01180.19820.00130.1245-0.2425-6.847417.3547
82.13960.6098-0.43151.2543-0.12940.469-0.012-0.2196-0.05210.0135-0.08920.10.0864-0.03280.13150.20850.0051-0.01690.21880.02160.1722-3.6361-14.939724.9149
93.2495-0.93340.48933.5794-0.26942.0789-0.0358-0.3567-0.02970.208-0.07040.18390.3763-0.04970.06310.23170.01330.02210.2806-0.00780.1539-5.6436-13.648431.5123
100.40310.0865-0.07922.07980.6341.3196-0.0209-0.04920.04970.03740.0599-0.01390.02750.0246-0.01770.12550.0089-0.00620.1330.00860.1228-15.10010.41750.4402
114.38570.9408-2.15511.2025-0.64382.1426-0.11410.1935-0.162-0.14790.0583-0.0250.1671-0.03520.06570.18290.0041-0.01510.1219-0.00330.1194-6.9455-16.3454-16.7963
122.0793-0.99990.05242.2064-0.01930.63610.01130.0915-0.0008-0.141-0.0144-0.0620.07980.01540.00920.1651-0.01340.00070.14990.00240.1052-2.6226-9.1096-15.6159
130.6932-0.2942-0.20431.1250.15840.4922-0.00970.07130.0286-0.12130.02450.00580.0186-0.0067-0.00470.1547-0.0069-0.0120.14450.01350.1183-9.0671-1.0754-13.6706
142.935-0.1201-1.19730.78650.13121.5781-0.079-0.0968-0.0110.05730.04150.09510.0628-0.07680.04530.1309-0.0031-0.02110.1141-0.01240.1328-16.61463.65712.3778
151.04430.11290.07991.237-0.05081.5433-0.0062-0.09240.15670.0171-0.0420.0744-0.1911-0.03390.03430.16640.0245-0.01030.1412-0.00670.2193-21.272315.17525.2067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 231 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 297 )
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 334 )
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 391 )
5X-RAY DIFFRACTION5chain 'A' and (resid 392 through 416 )
6X-RAY DIFFRACTION6chain 'A' and (resid 417 through 476 )
7X-RAY DIFFRACTION7chain 'A' and (resid 477 through 510 )
8X-RAY DIFFRACTION8chain 'A' and (resid 511 through 551 )
9X-RAY DIFFRACTION9chain 'A' and (resid 552 through 569 )
10X-RAY DIFFRACTION10chain 'B' and (resid 237 through 297 )
11X-RAY DIFFRACTION11chain 'B' and (resid 298 through 334 )
12X-RAY DIFFRACTION12chain 'B' and (resid 335 through 381 )
13X-RAY DIFFRACTION13chain 'B' and (resid 382 through 476 )
14X-RAY DIFFRACTION14chain 'B' and (resid 477 through 510 )
15X-RAY DIFFRACTION15chain 'B' and (resid 511 through 569 )

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