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- PDB-5lac: SeMet Labeled Derivative of Cavally Virus 3CL Protease -

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Basic information

Entry
Database: PDB / ID: 5lac
TitleSeMet Labeled Derivative of Cavally Virus 3CL Protease
Components3Cl Protease
KeywordsHYDROLASE / SeMet derivative / Protease / Mesonivirus / 3CL
Function / homology
Function and homology information


helicase activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase ...helicase activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / proteolysis / zinc ion binding / ATP binding / membrane
Similarity search - Function
Viral cysteine endopeptidase C107 / Viral cysteine endopeptidase C107 / LAP1C-like, C-terminal domain superfamily / : / DNA2/NAM7-like helicase / AAA domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. ...Viral cysteine endopeptidase C107 / Viral cysteine endopeptidase C107 / LAP1C-like, C-terminal domain superfamily / : / DNA2/NAM7-like helicase / AAA domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesCavally virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsKanitz, M. / Heine, A. / Diederich, W.E.
CitationJournal: Virology / Year: 2019
Title: Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus.
Authors: Kanitz, M. / Blanck, S. / Heine, A. / Gulyaeva, A.A. / Gorbalenya, A.E. / Ziebuhr, J. / Diederich, W.E.
History
DepositionJun 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
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 / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Nov 6, 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
A: 3Cl Protease
B: 3Cl Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0974
Polymers71,9132
Non-polymers1842
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-24 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.144, 111.353, 58.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 3Cl Protease


Mass: 35956.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SeMet derivative prepared for structure solution / Source: (gene. exp.) Cavally virus / Gene: pp1ab, CAVV_gp1 / Plasmid: MBP-pp1a-1387-1700 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / Variant (production host): Methionine Auxotroph / References: UniProt: F8RL29
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M Lithiumacetate, 24% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2014
RadiationMonochromator: Si111 DCM with sagital bender / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.94→40 Å / Num. obs: 44979 / % possible obs: 97 % / Redundancy: 4.6 % / Rsym value: 0.075 / Net I/σ(I): 21.1
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.5 / % possible all: 92.6

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Processing

Software
NameVersionClassification
AUTOMARdata collection
HKL-2000data reduction
SHELXDEphasing
PHENIXdev_1779refinement
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.94→35.946 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 2264 5.07 %Random Selection
Rwork0.1733 ---
obs0.175 44650 96.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→35.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 12 303 4855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084682
X-RAY DIFFRACTIONf_angle_d1.0656393
X-RAY DIFFRACTIONf_dihedral_angle_d10.9911622
X-RAY DIFFRACTIONf_chiral_restr0.047736
X-RAY DIFFRACTIONf_plane_restr0.005821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.98220.25171270.21222472X-RAY DIFFRACTION93
1.9822-2.02830.25371400.20292490X-RAY DIFFRACTION93
2.0283-2.0790.27081240.19662500X-RAY DIFFRACTION92
2.079-2.13520.23941280.1892521X-RAY DIFFRACTION94
2.1352-2.1980.22671540.17782523X-RAY DIFFRACTION95
2.198-2.2690.24761430.19262559X-RAY DIFFRACTION95
2.269-2.350.23541650.18212611X-RAY DIFFRACTION97
2.35-2.44410.25821270.17932666X-RAY DIFFRACTION98
2.4441-2.55530.19121470.17632684X-RAY DIFFRACTION99
2.5553-2.690.23341570.17942702X-RAY DIFFRACTION100
2.69-2.85850.21631170.18242750X-RAY DIFFRACTION100
2.8585-3.07910.2561600.18782726X-RAY DIFFRACTION100
3.0791-3.38870.20441430.17462747X-RAY DIFFRACTION100
3.3887-3.87860.17081590.16242726X-RAY DIFFRACTION100
3.8786-4.88470.15451400.13532812X-RAY DIFFRACTION100
4.8847-35.95260.18641330.17912897X-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)
10.10740.0904-0.20640.2271-0.21540.3275-0.1205-0.0382-0.052-0.09050.062-0.13670.00420.0293-0.00670.1788-0.00350.00370.1822-0.02110.217633.663433.788338.7006
20.2560.0750.0520.34220.06360.2577-0.0903-0.41210.05360.35790.0353-0.2634-0.25160.1783-0.02580.21260.0029-0.1010.2985-0.01070.293440.359239.645253.3654
30.43160.19580.24490.88620.39010.5223-0.05310.1277-0.04290.18840.1121-0.16440.00760.01620.06780.1306-0.0293-0.01930.14920.00080.166228.140132.447640.0673
40.04350.0579-0.08080.2860.11130.439-0.1688-0.15580.17990.2528-0.1574-0.3084-0.25310.2917-0.72090.5459-0.0272-0.2450.09410.19360.015718.16278.972652.5194
50.43440.30.05390.5931-0.01420.98430.0448-0.04380.01620.1742-0.05630.0560.1935-0.07780.02020.1686-0.03040.01440.14110.00570.159212.020814.382342.9211
60.01520.01390.00210.0177-0.0053-0.00250.0116-0.05090.03040.1613-0.4644-0.1918-0.3725-0.1292-0.00020.3935-0.0059-0.07630.6367-0.04040.51480.67124.261224.2939
70.1733-0.167-0.1690.2870.470.5566-0.0944-0.00580.00080.06220.0478-0.045-0.338-0.020700.2203-0.0511-0.01090.18420.01040.191119.538336.721317.1358
80.2769-0.1967-0.29450.13640.21720.340.1430.34230.33610.1228-0.12210.0125-0.6501-0.5458-0.01750.54030.0349-0.08420.35670.02590.42949.250443.72413.6619
90.5511-0.0192-0.16330.24540.11960.1004-0.25230.45110.5084-0.2336-0.1125-0.0173-0.5660.3075-0.16570.5478-0.1069-0.07830.26590.11950.281220.876946.3354.8171
100.18190.190.20550.25560.11970.3549-0.0425-0.02020.0735-0.0580.11810.0104-0.10910.07170.00040.2036-0.05130.0150.1901-0.00460.182523.037232.221919.2285
110.04180.0731-0.05490.0871-0.07830.06850.0060.17850.0832-0.4330.09320.19190.0572-0.04660.00020.265-0.0212-0.03770.1911-0.00550.214518.2479.91778.7517
120.4265-0.05480.16430.6844-0.10190.5469-0.03570.0712-0.0663-0.03050.0523-0.1543-0.03120.13950.00430.12350.0035-0.01040.1806-0.05110.185127.00849.85416.4497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:41)
2X-RAY DIFFRACTION2(chain A and resid 42:94)
3X-RAY DIFFRACTION3(chain A and resid 95:175)
4X-RAY DIFFRACTION4(chain A and resid 176:195)
5X-RAY DIFFRACTION5(chain A and resid 196:303)
6X-RAY DIFFRACTION6(chain A and resid 304:314)
7X-RAY DIFFRACTION7(chain B and resid 1:50)
8X-RAY DIFFRACTION8(chain B and resid 51:78)
9X-RAY DIFFRACTION9(chain B and resid 79:99)
10X-RAY DIFFRACTION10(chain B and resid 100:168)
11X-RAY DIFFRACTION11(chain B and resid 169:189)
12X-RAY DIFFRACTION12(chain B and resid 190:305)

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