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- PDB-6xa9: SARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargy... -

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Basic information

Entry
Database: PDB / ID: 6xa9
TitleSARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargylamide
Components
  • ISG15 CTD-propargylamide
  • Non-structural protein 3
KeywordsHYDROLASE/SUBSTRATE / SARS CoV-2 / papain-like protease / ISG15CTD activity based probe / COVID19 / HYDROLASE-SUBSTRATE complex
Function / homology
Function and homology information


positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / positive regulation of interleukin-10 production ...positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / modification-dependent protein catabolic process / ISG15 antiviral mechanism / protein tag activity / positive regulation of type II interferon production / Interferon alpha/beta signaling / integrin binding / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / defense response to virus / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / defense response to bacterium / copper ion binding / symbiont-mediated activation of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / cysteine-type endopeptidase activity / viral RNA genome replication / DNA clamp loader activity / innate immune response / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / : / ubiquitin protein ligase binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity
Similarity search - Function
Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / : / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain / Ubiquitin-like (UB roll) / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus ...Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / : / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain / Ubiquitin-like (UB roll) / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Ubiquitin family / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Ubiquitin homologues / Ubiquitin domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile.
Similarity search - Domain/homology
Ubiquitin-like protein ISG15 / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKlemm, T. / Calleja, D.J. / Richardson, L.W. / Lechtenberg, B.C. / Komander, D.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1178122 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT2002119 Australia
Citation
Journal: Embo J. / Year: 2020
Title: Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2.
Authors: Klemm, T. / Ebert, G. / Calleja, D.J. / Allison, C.C. / Richardson, L.W. / Bernardini, J.P. / Lu, B.G. / Kuchel, N.W. / Grohmann, C. / Shibata, Y. / Gan, Z.Y. / Cooney, J.P. / Doerflinger, M. ...Authors: Klemm, T. / Ebert, G. / Calleja, D.J. / Allison, C.C. / Richardson, L.W. / Bernardini, J.P. / Lu, B.G. / Kuchel, N.W. / Grohmann, C. / Shibata, Y. / Gan, Z.Y. / Cooney, J.P. / Doerflinger, M. / Au, A.E. / Blackmore, T.R. / van der Heden van Noort, G.J. / Geurink, P.P. / Ovaa, H. / Newman, J. / Riboldi-Tunnicliffe, A. / Czabotar, P.E. / Mitchell, J.P. / Feltham, R. / Lechtenberg, B.C. / Lowes, K.N. / Dewson, G. / Pellegrini, M. / Lessene, G. / Komander, D.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionJun 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com
Item: _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name
Revision 1.4Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 16, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 3
B: ISG15 CTD-propargylamide
C: Non-structural protein 3
D: ISG15 CTD-propargylamide
E: Non-structural protein 3
F: ISG15 CTD-propargylamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,95517
Polymers135,0226
Non-polymers93311
Water54030
1
A: Non-structural protein 3
B: ISG15 CTD-propargylamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3496
Polymers45,0072
Non-polymers3424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-6 kcal/mol
Surface area18130 Å2
MethodPISA
2
C: Non-structural protein 3
D: ISG15 CTD-propargylamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3496
Polymers45,0072
Non-polymers3424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-7 kcal/mol
Surface area18000 Å2
MethodPISA
3
E: Non-structural protein 3
F: ISG15 CTD-propargylamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2575
Polymers45,0072
Non-polymers2503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-5 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.172, 124.172, 238.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEHISHIS(chain 'A' and ((resid 5 through 7 and (name N...AA5 - 508 - 53
12LYSLYSASNASN(chain 'A' and ((resid 5 through 7 and (name N...AA53 - 26756 - 270
13GLNGLNTHRTHR(chain 'A' and ((resid 5 through 7 and (name N...AA269 - 313272 - 316
14HOHHOHHOHHOH(chain 'A' and ((resid 5 through 7 and (name N...AR503 - 504
25ILEILEHISHIS(chain 'C' and ((resid 5 through 7 and (name N...CC5 - 508 - 53
26LYSLYSASNASN(chain 'C' and ((resid 5 through 7 and (name N...CC53 - 26756 - 270
27GLNGLNTHRTHR(chain 'C' and ((resid 5 through 7 and (name N...CC269 - 313272 - 316
28HOHHOHHOHHOH(chain 'C' and ((resid 5 through 7 and (name N...CT503 - 504
39ILEILEHISHIS(chain 'E' and (resid 5 through 142 or (resid 143...EE5 - 508 - 53
310LYSLYSASNASN(chain 'E' and (resid 5 through 142 or (resid 143...EE53 - 26756 - 270
311GLNGLNTHRTHR(chain 'E' and (resid 5 through 142 or (resid 143...EE269 - 313272 - 316
312GOLGOLGOLGOL(chain 'E' and (resid 5 through 142 or (resid 143...EP - Q502 - 503

NCS ensembles :
ID
1
2

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Components

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


Mass: 35982.863 Da / Num. of mol.: 3 / Fragment: UNP residues 1563-1878
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein ISG15 CTD-propargylamide / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein / hUCRP


Mass: 9024.344 Da / Num. of mol.: 3 / Fragment: C-terminal domain (UNP residues 79-157) / Mutation: G176 replaced with propargylamide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Production host: Escherichia coli (E. coli) / References: UniProt: P05161
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M lithium sulfate, 25% PEG3350, 0.1 M Bis-Tris chloride, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→49.28 Å / Num. obs: 42170 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 91.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.163 / Net I/σ(I): 10.5
Reflection shellResolution: 2.9→3.01 Å / Redundancy: 14.2 % / Rmerge(I) obs: 2.876 / Num. unique obs: 4344 / CC1/2: 0.496 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 6WRH & 6FFA

6wrh

6ffa


Resolution: 2.9→49.28 Å / SU ML: 0.3948 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3839
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 1978 4.7 %
Rwork0.1997 40081 -
obs0.2011 42059 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8876 0 51 30 8957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00599139
X-RAY DIFFRACTIONf_angle_d0.939212464
X-RAY DIFFRACTIONf_chiral_restr0.05281414
X-RAY DIFFRACTIONf_plane_restr0.00721609
X-RAY DIFFRACTIONf_dihedral_angle_d11.36515344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.38341390.36732800X-RAY DIFFRACTION99.76
2.97-3.050.32891400.31072824X-RAY DIFFRACTION99.9
3.05-3.140.32741380.28892798X-RAY DIFFRACTION100
3.14-3.240.26431400.2472821X-RAY DIFFRACTION99.97
3.24-3.360.30561410.22482836X-RAY DIFFRACTION99.87
3.36-3.490.24951380.21092798X-RAY DIFFRACTION100
3.49-3.650.24151420.20532860X-RAY DIFFRACTION99.9
3.65-3.850.20931380.18842825X-RAY DIFFRACTION99.93
3.85-4.090.20221400.17632841X-RAY DIFFRACTION100
4.09-4.40.19481410.16212868X-RAY DIFFRACTION100
4.4-4.840.18211420.15292863X-RAY DIFFRACTION99.97
4.84-5.550.18181440.17262910X-RAY DIFFRACTION100
5.55-6.980.26761440.22432937X-RAY DIFFRACTION100
6.98-49.280.24391510.20623100X-RAY DIFFRACTION99.63
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)
11.583951245280.140067721447-0.1580614760772.496626501720.5257514781532.205510143050.05799587017650.120426857165-0.0392660018475-0.08361707101420.0050589296180.05746595732070.2082783036390.2145323070634.64685769085E-50.4542505941060.0956398704758-0.008997265818270.6178727228650.005410079641680.47586332468-25.79546570265.97780845652-38.6640764189
20.5332754923410.2461872029390.9068935344810.7728867974750.5600230107451.727793124910.16307722139-0.215472590830.244947844305-0.701806812013-0.04769931379390.4586734711340.28465311494-0.04140109761692.34724088371E-60.7935356892580.0137152688848-0.05268473566640.746759768976-0.08214180676590.739070060988-39.23598416088.4374083094-56.7224800703
32.57226148738-1.41703784951-0.4829474655162.901148705080.2548424397571.32443580554-0.169350595906-0.271487477794-0.4107591271030.06558386593470.1634363464260.3144139466580.0731193859045-0.170498801489-0.03875687003850.398586073439-0.05861031098280.0232868852390.5742803528490.1029449599750.578366210671-61.20671403146.46262063651-24.5142412392
40.668240467437-0.2506438019940.1568376363471.245692716950.6273392444251.1340351082-0.0113349252493-1.085147209970.01095215141920.2051931590630.329443961615-0.1334654560780.0298214373529-0.6807589137940.2139351440390.6278893448510.2235396555050.05519114741291.261937521810.249525093160.677966978982-47.93771340354.25367989904-6.55263518674
52.50350392667-0.1092980379-0.05221639476531.27639296392-1.535493572072.41763152281-0.181677760998-0.5939644523440.1354937798970.5226934913950.2117511347540.0481879925855-0.491045748046-0.009406367264130.1091482621760.8804674391320.282737385624-0.09171319127530.931957456731-0.01867779147310.610048085891-19.99256583281.080456454974.48285645127
60.989002865029-0.4910910262840.5426647743320.462503992477-0.2147658609540.5253273942820.386398488737-0.6593127208070.370181587820.08284569421940.2425142115490.709573508803-1.37739944189-0.9796617190940.3040504186121.590421756770.2864708459130.1969809463861.21353916525-0.2718616147260.926915708394-28.245515357616.327979626917.9277134471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 314)
2X-RAY DIFFRACTION2(chain 'B' and resid 78 through 156)
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 314)
4X-RAY DIFFRACTION4(chain 'D' and resid 79 through 157)
5X-RAY DIFFRACTION5(chain 'E' and resid 5 through 313)
6X-RAY DIFFRACTION6(chain 'F' and resid 79 through 157)

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