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- PDB-6lj9: Crystal Structure of Se-Met ASFV pS273R protease -

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Basic information

Entry
Database: PDB / ID: 6lj9
TitleCrystal Structure of Se-Met ASFV pS273R protease
ComponentsCysteine protease S273R
KeywordsHYDROLASE
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: 2.307 Å
AuthorsLi, G.B. / Liu, X.X. / 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: 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: RCSB
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

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Assembly

Deposited unit
B: Cysteine protease S273R
A: Cysteine protease S273R


Theoretical massNumber of molelcules
Total (without water)65,8302
Polymers65,8302
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-2 kcal/mol
Surface area24990 Å2
Unit cell
Length a, b, c (Å)60.165, 83.280, 108.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine protease S273R / pS273R


Mass: 32915.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus pig/Kenya/KEN-50/1950
Strain: isolate 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 / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsAuthors states that they modeled the MSE residues (114A, 115A) in the place with a good quality ...Authors states that they modeled the MSE residues (114A, 115A) in the place with a good quality electron density. Thus, there have both the Met and Mse residues in the coordinates.

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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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris, pH 8.2, 23% w/v Polyethylene glycol 1,500
PH range: 8.0-8.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.079→48.843 Å / Num. obs: 21872 / % possible obs: 100 % / Redundancy: 7.04 % / CC1/2: 0.999 / Net I/σ(I): 10.67
Reflection shellResolution: 2.079→2.2 Å / Num. unique obs: 19824 / CC1/2: 0.715

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.307→48.769 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 1093 5 %
Rwork0.1914 20779 -
obs0.1929 21872 88.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.15 Å2 / Biso mean: 47.3544 Å2 / Biso min: 9.04 Å2
Refinement stepCycle: final / Resolution: 2.307→48.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4321 0 0 108 4429
Biso mean---41.8 -
Num. residues----531
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.307-2.41150.27841000.2422178762
2.4115-2.53860.3361970.2324209772
2.5386-2.69770.31291270.2276236082
2.6977-2.90590.24641400.2329275695
2.9059-3.19830.25391510.21442944100
3.1983-3.6610.20561550.18732908100
3.661-4.61190.17551600.1555293499
4.6119-48.7690.19871630.1756299397
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)
10.30550.1249-0.09630.2111-0.06180.02280.22370.02250.5645-0.0345-0.18050.6140.2689-0.19790.04690.18270.0345-0.11460.22270.08010.063-17.6282-24.9238-27.9318
20.11460.0115-0.08610.0862-0.02030.0275-0.45210.37490.0512-0.44140.05560.1568-0.12550.2045-0.12870.28660.0328-0.01410.18370.2115-0.23664.2534-15.6838-29.1685
30.4830.16080.14490.5548-0.31220.4615-0.02590.0833-0.0330.0122-0.0169-0.13050.00430.1023-0.04460.1434-0.0077-0.03090.14320.02170.09639.7643-20.5435-21.1658
40.1502-0.21650.03880.21020.0110.0886-0.00560.0693-0.0859-0.035-0.08810.2842-0.0392-0.009-0.00440.17210.0136-0.0230.22260.04420.3688-18.85248.455-4.0136
50.02480.01830.00240.04980.0217-0.0087-0.0576-0.0060.07610.05920.00360.3785-0.1312-0.08310.00010.1504-0.02060.0510.18-0.00790.1669-5.8786-4.91824.8349
60.3615-0.0142-0.02070.0224-0.05440.00760.0026-0.2197-0.20660.2932-0.1087-0.0267-0.0080.115-0.02480.2036-0.0406-0.00390.19740.03680.1792-0.529-10.28458.9781
70.29110.08720.06170.23750.0230.49990.00130.00640.24150.0296-0.0093-0.30310.02790.0961-0.02330.06770.0083-0.01780.0925-0.00190.19088.0643-1.41243.1431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 89 )B2 - 89
2X-RAY DIFFRACTION2chain 'B' and (resid 90 through 128 )B90 - 128
3X-RAY DIFFRACTION3chain 'B' and (resid 129 through 273 )B129 - 273
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 89 )A2 - 89
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 117 )A90 - 117
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 175 )A118 - 175
7X-RAY DIFFRACTION7chain 'A' and (resid 176 through 273 )A176 - 273

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