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- PDB-8cx9: Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeri... -

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Basic information

Entry
Database: PDB / ID: 8cx9
TitleStructure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism
Components
  • Papain-like protease nsp3
  • Ubiquitin variant UbV.CV2.1
KeywordsVIRAL PROTEIN/SIGNALING PROTEIN / inhibitor complex / allosteric inhibition / VIRAL PROTEIN / VIRAL PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression ...Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / cytosolic ribosome / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / viral genome replication / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / methyltransferase activity / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling
Similarity search - Function
Jelly Rolls - #1680 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family ...Jelly Rolls - #1680 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain
Similarity search - Domain/homology
BROMIDE ION / Replicase polyprotein 1a / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSinger, A.U. / Slater, C.L. / Patel, A. / Russel, R. / Mark, B.L. / Sidhu, S.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)OV3-170346 Canada
CitationJournal: Plos Pathog. / Year: 2022
Title: Ubiquitin variants potently inhibit SARS-CoV-2 PLpro and viral replication via a novel site distal to the protease active site.
Authors: van Vliet, V.J.E. / Huynh, N. / Pala, J. / Patel, A. / Singer, A. / Slater, C. / Chung, J. / van Huizen, M. / Teyra, J. / Miersch, S. / Luu, G.K. / Ye, W. / Sharma, N. / Ganaie, S.S. / ...Authors: van Vliet, V.J.E. / Huynh, N. / Pala, J. / Patel, A. / Singer, A. / Slater, C. / Chung, J. / van Huizen, M. / Teyra, J. / Miersch, S. / Luu, G.K. / Ye, W. / Sharma, N. / Ganaie, S.S. / Russell, R. / Chen, C. / Maynard, M. / Amarasinghe, G.K. / Mark, B.L. / Kikkert, M. / Sidhu, S.S.
History
DepositionMay 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Papain-like protease nsp3
A: Papain-like protease nsp3
C: Papain-like protease nsp3
D: Papain-like protease nsp3
E: Ubiquitin variant UbV.CV2.1
I: Ubiquitin variant UbV.CV2.1
F: Ubiquitin variant UbV.CV2.1
G: Ubiquitin variant UbV.CV2.1
K: Ubiquitin variant UbV.CV2.1
L: Ubiquitin variant UbV.CV2.1
H: Ubiquitin variant UbV.CV2.1
J: Ubiquitin variant UbV.CV2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,77325
Polymers237,95012
Non-polymers82213
Water00
1
B: Papain-like protease nsp3
F: Ubiquitin variant UbV.CV2.1
G: Ubiquitin variant UbV.CV2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7136
Polymers59,4883
Non-polymers2253
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Papain-like protease nsp3
E: Ubiquitin variant UbV.CV2.1
I: Ubiquitin variant UbV.CV2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8168
Polymers59,4883
Non-polymers3285
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Papain-like protease nsp3
K: Ubiquitin variant UbV.CV2.1
L: Ubiquitin variant UbV.CV2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5765
Polymers59,4883
Non-polymers882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Papain-like protease nsp3
H: Ubiquitin variant UbV.CV2.1
J: Ubiquitin variant UbV.CV2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6686
Polymers59,4883
Non-polymers1813
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.580, 174.860, 121.560
Angle α, β, γ (deg.)90.000, 95.740, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 or (resid 5 through 6...
d_2ens_1(chain "B" and (resid 4 or (resid 5 through 6...
d_3ens_1(chain "C" and (resid 4 through 42 or (resid 43...
d_4ens_1(chain "D" and (resid 4 or (resid 5 through 6...
d_1ens_2(chain "E" and (resid 1 or (resid 2 and (name...
d_2ens_2(chain "F" and (resid 1 or (resid 2 and (name...
d_3ens_2(chain "G" and (resid 1 through 5 or (resid 6...
d_4ens_2(chain "H" and (resid 1 or (resid 2 and (name...
d_5ens_2(chain "I" and (resid 1 or (resid 2 and (name...
d_6ens_2(chain "J" and (resid 1 or (resid 2 and (name...
d_7ens_2(chain "K" and (resid 1 through 5 or (resid 6...
d_8ens_2(chain "L" and (resid 1 or (resid 2 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRCYSB3 - 191
d_12ens_1GLNILEB193 - 313
d_21ens_1THRCYSA3 - 191
d_22ens_1GLNILEA193 - 313
d_31ens_1THRCYSC1 - 189
d_32ens_1GLNILEC191 - 311
d_41ens_1THRILED1 - 310
d_11ens_2METILEE1 - 61
d_12ens_2LYSLEUE63 - 73
d_21ens_2METILEG1 - 61
d_22ens_2LYSLEUG63 - 73
d_31ens_2METILEH2 - 62
d_32ens_2LYSLEUH64 - 74
d_41ens_2METILEX1 - 61
d_42ens_2LYSLEUX63 - 73
d_51ens_2METILEF2 - 62
d_52ens_2LYSLEUF64 - 74
d_61ens_2METILEY1 - 61
d_62ens_2LYSLEUY63 - 73
d_71ens_2METILEI1 - 61
d_72ens_2LYSLEUI63 - 73
d_81ens_2METILEJ1 - 61
d_82ens_2LYSLEUJ63 - 73

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.941651296609, 0.281331001763, -0.184785559612), (-0.290933838163, -0.956375608655, 0.0265178615624), (-0.169264105487, 0.0787309508185, 0.982421040072)27.0839525094, -34.2487668668, -27.7831751844
2given(-0.95075824198, -0.26846857296, -0.154865718091), (0.260517599136, -0.962933925975, 0.0699202027113), (-0.167896830963, 0.0261319639432, 0.985458154674)10.3188041206, -37.5415953082, 33.1075007744
3given(0.882513072235, -0.469553360538, 0.0262739213186), (0.469325090403, 0.88290389186, 0.014651868726), (-0.030077181585, -0.000599455185308, 0.999547399477)-13.81112531, -4.23599930431, 59.8992919849
4given(-0.945116675458, 0.28406484503, -0.161436159483), (-0.291234444805, -0.956395781296, 0.0221270802213), (-0.148111336264, 0.0679284427747, 0.986635068671)25.273306352, -33.5056602687, -28.6347043304
5given(0.0256487288955, -0.769217384449, 0.638472206261), (-0.763207091843, 0.397429993058, 0.509474568136), (-0.645644699247, -0.50035389084, -0.576878588834)-71.2011302526, -6.62568503371, 47.7178480706
6given(0.858195076532, -0.513301500439, -0.00477286746963), (0.51329868419, 0.858024401107, 0.0178490311487), (-0.0050666977178, -0.0177678572446, 0.999829301343)-1.32961186264, -5.99151555811, -61.8247311221
7given(0.308778590368, 0.656239002022, -0.688481048653), (0.684596089876, -0.655850751924, -0.318100589323), (-0.660290826725, -0.373108782295, -0.651771325479)72.3152891775, -51.3097827141, 90.332284136
8given(-0.0811587422072, 0.903474589162, -0.420888257501), (0.741951364753, -0.227204048636, -0.630782444766), (-0.665523426263, -0.363472126885, -0.651894609637)86.3473118158, -11.2324945497, 29.7277659369
9given(-0.971237566908, -0.216125149107, -0.0999375232286), (0.211628115462, -0.975872380209, 0.0537274444886), (-0.109138120617, 0.0310325227565, 0.993542074177)9.08738161084, -37.0029018801, 33.0142600525
10given(-0.379686601235, -0.47345981334, 0.79477914542), (-0.641802735092, 0.753552543786, 0.142294810104), (-0.66627872101, -0.456063996503, -0.58998160736)-59.1723573844, 31.8625353096, 114.015535056

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Components

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Protein , 2 types, 12 molecules BACDEIFGKLHJ

#1: Protein
Papain-like protease nsp3 / Non-structural protein 3 / nsp3 / PL2-PRO / Papain-like proteinase / PL-PRO


Mass: 36082.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Details (production host): pET-24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
References: UniProt: P0DTC1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein
Ubiquitin variant UbV.CV2.1 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 11702.310 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA52, UBCEP2 / Plasmid: pET-53-DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P62987

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Non-polymers , 4 types, 13 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Details

Has ligand of interestY
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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 14.86 mg/ml SARS-CoV2C111S/UbV.CV2.1, 20% PEG 3350, 0.2 M sodium bromide, 0.1 M BIS-TRIS propane (pH 6.3), 50 mM lithium chloride. Cryoprotected in the same buffer plus 30% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 20, 2021 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 3.5→49.74 Å / Num. obs: 23394 / % possible obs: 81.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 61.47 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.122 / Rrim(I) all: 0.174 / Χ2: 0.76 / Net I/σ(I): 6.4
Reflection shellResolution: 3.5→3.71 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2882 / CC1/2: 0.8 / Rpim(I) all: 0.375 / Rrim(I) all: 0.532 / Χ2: 0.73 / % possible all: 63

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CJM for the COVID19 PLPro, SWISS-MODEL model for the Ubv

7cjm


Resolution: 3.5→47.79 Å / SU ML: 0.4877 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.6346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2697 1998 8.56 %
Rwork0.2249 21342 -
obs0.2286 23340 81.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.1 Å2
Refinement stepCycle: LAST / Resolution: 3.5→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13976 0 13 0 13989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005214239
X-RAY DIFFRACTIONf_angle_d0.954219374
X-RAY DIFFRACTIONf_chiral_restr0.05382277
X-RAY DIFFRACTIONf_plane_restr0.01142481
X-RAY DIFFRACTIONf_dihedral_angle_d4.5811982
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.873428422098
ens_1d_3BX-RAY DIFFRACTIONTorsion NCS0.998656084464
ens_1d_4BX-RAY DIFFRACTIONTorsion NCS0.963958943993
ens_2d_2EX-RAY DIFFRACTIONTorsion NCS0.892410658603
ens_2d_3EX-RAY DIFFRACTIONTorsion NCS1.5567232883
ens_2d_4EX-RAY DIFFRACTIONTorsion NCS0.991990550596
ens_2d_5EX-RAY DIFFRACTIONTorsion NCS1.74747181453
ens_2d_6EX-RAY DIFFRACTIONTorsion NCS1.55691839021
ens_2d_7EX-RAY DIFFRACTIONTorsion NCS1.19189315152
ens_2d_8EX-RAY DIFFRACTIONTorsion NCS1.62463531102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.37191070.28781141X-RAY DIFFRACTION60.97
3.59-3.680.28931100.26411182X-RAY DIFFRACTION62.99
3.68-3.790.27351120.25341189X-RAY DIFFRACTION64.53
3.79-3.910.32451140.26891210X-RAY DIFFRACTION64.97
3.92-4.060.28871200.24581302X-RAY DIFFRACTION69.95
4.06-4.220.34351310.22551394X-RAY DIFFRACTION74.5
4.22-4.410.2671420.2181511X-RAY DIFFRACTION82.2
4.41-4.640.251550.2031659X-RAY DIFFRACTION88.57
4.64-4.930.22521630.21091746X-RAY DIFFRACTION92.76
4.93-5.310.27911670.221777X-RAY DIFFRACTION95.43
5.31-5.850.27081670.24211787X-RAY DIFFRACTION96.11
5.85-6.690.30431700.24191821X-RAY DIFFRACTION96.6
6.69-8.420.26411680.22491790X-RAY DIFFRACTION96.12
8.42-47.790.21491720.18341833X-RAY DIFFRACTION95.75

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