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- PDB-6ljb: Crystal Structure of ASFV pS273R protease -

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Basic information

Entry
Database: PDB / ID: 6ljb
TitleCrystal Structure of ASFV pS273R protease
ComponentsCysteine protease S273R
KeywordsHYDROLASE / ASFV / pS273R protease
Function / homology
Function and homology information


virion component / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / viral protein processing / cysteine-type endopeptidase activity / proteolysis
Similarity search - Function
Cysteine protease S273R / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
SUMO-1 cysteine protease S273R
Similarity search - Component
Biological speciesAfrican swine fever virus pig/Kenya/KEN-50/1950
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.487 Å
AuthorsLi, G.B. / Liu, X.X. / Chen, C. / Guo, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670731 China
National Natural Science Foundation of China (NSFC)31870733 China
CitationJournal: J.Virol. / Year: 2020
Title: Crystal Structure of African Swine Fever Virus pS273R Protease and Implications for Inhibitor Design.
Authors: Li, G. / Liu, X. / Yang, M. / Zhang, G. / Wang, Z. / Guo, K. / Gao, Y. / Jiao, P. / Sun, J. / Chen, C. / Wang, H. / Deng, W. / Xiao, H. / Li, S. / Wu, H. / Wang, Y. / Cao, L. / Jia, Z. / ...Authors: Li, G. / Liu, X. / Yang, M. / Zhang, G. / Wang, Z. / Guo, K. / Gao, Y. / Jiao, P. / Sun, J. / Chen, C. / Wang, H. / Deng, W. / Xiao, H. / Li, S. / Wu, H. / Wang, Y. / Cao, L. / Jia, Z. / Shang, L. / Yang, C. / Guo, Y. / Rao, Z.
History
DepositionDec 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 13, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine protease S273R


Theoretical massNumber of molelcules
Total (without water)32,7271
Polymers32,7271
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12710 Å2
Unit cell
Length a, b, c (Å)220.840, 37.988, 33.026
Angle α, β, γ (deg.)90.000, 93.440, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cysteine protease S273R / pS273R


Mass: 32727.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus pig/Kenya/KEN-50/1950
Strain: Pig/Kenya/KEN-50/1950 / Gene: Ken-123 / Production host: Escherichia coli (E. coli)
References: UniProt: P0C9B9, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.6 mM CoA, 0.2 M Ammonium acetate, 0.1 M Tris, pH8.5, 20% PEG3350.

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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: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0083 Å / Relative weight: 1
ReflectionResolution: 2.487→50 Å / Num. obs: 9380 / % possible obs: 95.2 % / Redundancy: 5.5 % / CC1/2: 0.993 / Net I/σ(I): 11.68
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 418 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.487→36.74 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 467 5.35 %
Rwork0.223 8254 -
obs0.2245 8721 88.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.59 Å2 / Biso mean: 39.3839 Å2 / Biso min: 16.68 Å2
Refinement stepCycle: final / Resolution: 2.487→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 0 78 2255
Biso mean---36.57 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.487-2.84650.29661050.2751212069
2.8465-3.58590.26811640.2397304598
3.5859-36.740.23511980.2015308998
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)
10.1444-0.1541-0.15090.11640.12060.1533-0.08030.3711-0.00910.15490.2418-0.4828-0.0579-0.50610.0040.2764-0.0570.03580.432-0.08920.379819.9065-5.6449-4.7197
20.0855-0.0086-0.04830.09330.08180.10480.03470.5510.17270.08720.15650.22150.1762-0.8665-0.00050.48480.0068-0.00770.55590.02480.60034.1784-11.56066.9931
30.12230.0144-0.06250.1211-0.03540.05620.1038-0.4169-0.28270.47970.12390.5516-0.0317-0.3643-0.00080.48660.05560.05030.51670.16080.53119.0369-10.618615.6879
40.20960.1670.09110.1749-0.04870.07660.0239-0.0413-0.2572-0.019-0.13350.09750.0358-0.0521-0.00150.22080.02170.02290.21850.00180.221825.5305-1.95225.6441
50.19560.09260.03080.04550.08830.13380.1082-0.42770.03330.16860.164-0.3160.04210.06410.00030.35840.0424-0.01380.3397-0.00230.334444.01330.883310.0522
60.72570.0546-0.18111.26830.61060.43160.274-0.4127-0.2365-0.0954-0.0167-0.36950.5608-0.03810.42330.388-0.0207-0.01840.32940.09060.294937.4709-12.00778.7351
70.48680.1314-0.01870.3683-0.40910.3487-0.0240.10390.0235-0.137-0.02940.1991-0.29260.0388-0.00010.3121-0.0117-0.04490.28-0.00670.320239.29414.9824-0.4931
80.5394-0.0405-0.22370.726-0.95661.6050.1165-0.08830.00470.0877-0.0089-0.4615-0.18590.9069-0.09760.18740.0144-0.00840.388-0.00920.298751.17292.56531.7356
90.49590.1340.28490.0721-0.07320.47270.00880.19330.0577-0.13570.00210.11730.0094-0.061300.29030.00210.00330.2860.00890.261234.84816.3777-6.9685
100.32060.0024-0.42330.21040.34221.2928-0.2523-0.03970.1020.0559-0.26130.32930.0923-0.5865-0.20110.31950.03490.00070.34940.02360.33119.62545.8745-0.9488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )A2 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 47 )A22 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 73 )A48 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 109 )A74 - 109
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 134 )A110 - 134
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 151 )A135 - 151
7X-RAY DIFFRACTION7chain 'A' and (resid 152 through 194 )A152 - 194
8X-RAY DIFFRACTION8chain 'A' and (resid 195 through 210 )A195 - 210
9X-RAY DIFFRACTION9chain 'A' and (resid 211 through 258 )A211 - 258
10X-RAY DIFFRACTION10chain 'A' and (resid 259 through 273 )A259 - 273

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