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- PDB-7ofu: Structure of SARS-CoV-2 Papain-like protease PLpro in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7ofu
TitleStructure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, methyl ester
ComponentsPapain-like protease nsp3
KeywordsHYDROLASE / HYDROLASE Papain-like protease PLpro Complex
Function / homology
Function and homology information


viral genome replication / methyltransferase 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 / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase 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 / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane
Similarity search - Function
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. ...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 Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
methyl 3,4-bis(oxidanyl)benzoate / PHOSPHATE ION / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsSrinivasan, V. / Ewert, W. / Werner, N. / Falke, S. / Guenther, S. / Reinke, P. / Sprenger, J. / Brognaro, H. / Ullah, N. / Andaleeb, H. ...Srinivasan, V. / Ewert, W. / Werner, N. / Falke, S. / Guenther, S. / Reinke, P. / Sprenger, J. / Brognaro, H. / Ullah, N. / Andaleeb, H. / Perbandt, M. / Alves Franca, B. / Schwinzer, M. / Wang, M. / Wolf, M. / Lieske, J. / Koua, F. / Ginn, H. / Lane, T.J. / Yefanov, O. / Gelisio, L. / Hakanpaeae, J. / Saouane, S. / Tolstikova, A. / Groessler, M. / Fleckenstein, H. / Trost, F. / Lorenzen, K. / Schubert, R. / Han, H. / Schmidt, C. / Brings, L. / Galchenkova, M. / Gevorkov, Y. / Li, C. / Perk, A. / Awel, S. / Wahab, A. / Choudary, I. / Turk, D. / Hinrichs, W. / Chapman, H.N. / Meents, A. / Betzel, C.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2056 - project ID 390715994 Germany
European CommissionEU project 101003551 - EXSCALATE4CoV (E4C)European Union
CitationJournal: Commun Biol / Year: 2022
Title: Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.
Authors: Srinivasan, V. / Brognaro, H. / Prabhu, P.R. / de Souza, E.E. / Gunther, S. / Reinke, P.Y.A. / Lane, T.J. / Ginn, H. / Han, H. / Ewert, W. / Sprenger, J. / Koua, F.H.M. / Falke, S. / Werner, ...Authors: Srinivasan, V. / Brognaro, H. / Prabhu, P.R. / de Souza, E.E. / Gunther, S. / Reinke, P.Y.A. / Lane, T.J. / Ginn, H. / Han, H. / Ewert, W. / Sprenger, J. / Koua, F.H.M. / Falke, S. / Werner, N. / Andaleeb, H. / Ullah, N. / Franca, B.A. / Wang, M. / Barra, A.L.C. / Perbandt, M. / Schwinzer, M. / Schmidt, C. / Brings, L. / Lorenzen, K. / Schubert, R. / Machado, R.R.G. / Candido, E.D. / Oliveira, D.B.L. / Durigon, E.L. / Niebling, S. / Garcia, A.S. / Yefanov, O. / Lieske, J. / Gelisio, L. / Domaracky, M. / Middendorf, P. / Groessler, M. / Trost, F. / Galchenkova, M. / Mashhour, A.R. / Saouane, S. / Hakanpaa, J. / Wolf, M. / Alai, M.G. / Turk, D. / Pearson, A.R. / Chapman, H.N. / Hinrichs, W. / Wrenger, C. / Meents, A. / Betzel, C.
History
DepositionMay 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 24, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_name_com / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / struct_conf / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_name_com.name / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _reflns_shell.number_unique_obs / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 3.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / citation / citation_author / entity / entity_src_gen / exptl / pdbx_contact_author / pdbx_database_related / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conn / struct_keywords
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _atom_type.scat_Cromer_Mann_a1 / _atom_type.scat_Cromer_Mann_a2 / _atom_type.scat_Cromer_Mann_a3 / _atom_type.scat_Cromer_Mann_c / _citation.title / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _exptl.crystals_number / _pdbx_contact_author.address_1 / _pdbx_contact_author.address_2 / _pdbx_contact_author.address_3 / _pdbx_contact_author.email / _pdbx_contact_author.phone / _pdbx_contact_author.postal_code / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_restr.type / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_low / _reflns.pdbx_CC_half / _reflns.pdbx_CC_star / _reflns.percent_possible_obs / _reflns_shell.pdbx_CC_star / _reflns_shell.percent_possible_all / _software.version / _struct_conn.pdbx_dist_value / _struct_keywords.text
Provider: author / Type: Coordinate replacement
Revision 3.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 3.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Papain-like protease nsp3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,50510
Polymers35,6721
Non-polymers8339
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.391, 82.391, 134.132
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules AAA

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


Mass: 35671.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTC1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Non-polymers , 6 types, 339 molecules

#2: Chemical ChemComp-HE9 / methyl 3,4-bis(oxidanyl)benzoate


Mass: 168.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir ...Details: Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir solution consisting of 1.0M NaH2PO4/1.0MKH2PO4, 100mM Tris_HCl pH=7.5. This growth solution was equilibrated by sitting drop vapor diffusion against 80 uL reservoir solution. Prior to crystallization 100 nL droplets of 10 mM compound solutions in DMSO were applied to the wells of SwissCI 96-well plates (2-well) and subsequently dried in vacuum.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.72→48.92 Å / Num. obs: 56596 / % possible obs: 99.954 % / Redundancy: 10.6 % / CC1/2: 1 / Net I/σ(I): 16.66
Reflection shellResolution: 1.72→1.782 Å / Redundancy: 10.9 % / Num. unique obs: 5573 / CC1/2: 0.576

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7nfv

7nfv


Resolution: 1.72→48.868 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.882 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.202 2834 5.008 %
Rwork0.1749 53754 -
all0.176 --
obs-56588 99.954 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.073 Å2-0.037 Å20 Å2
2---0.073 Å2-0 Å2
3---0.238 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 46 330 2878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132707
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152460
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.6623686
X-RAY DIFFRACTIONr_angle_other_deg1.5341.5825686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.10223.759133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35215454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.491159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023121
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02633
X-RAY DIFFRACTIONr_nbd_refined0.2180.2472
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.22235
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21264
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21322
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.130.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.215
X-RAY DIFFRACTIONr_nbd_other0.2210.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.223
X-RAY DIFFRACTIONr_mcbond_it2.1252.7351313
X-RAY DIFFRACTIONr_mcbond_other2.12.7331312
X-RAY DIFFRACTIONr_mcangle_it2.8154.0851657
X-RAY DIFFRACTIONr_mcangle_other2.8144.0891658
X-RAY DIFFRACTIONr_scbond_it3.7083.2351393
X-RAY DIFFRACTIONr_scbond_other3.5643.1891378
X-RAY DIFFRACTIONr_scangle_it5.454.6662029
X-RAY DIFFRACTIONr_scangle_other5.3654.5962006
X-RAY DIFFRACTIONr_lrange_it7.34633.1633083
X-RAY DIFFRACTIONr_lrange_other7.09232.3372983
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.72-1.7650.3861900.34139170.34341170.6050.62699.75710.321
1.765-1.8130.342080.31238270.31440350.7250.731000.286
1.813-1.8650.2861940.27537150.27539100.8240.83599.97440.242
1.865-1.9230.2612040.2436050.24138100.880.89499.97380.204
1.923-1.9860.2561610.22935300.2336920.9050.90499.97290.188
1.986-2.0550.2161600.18833970.18935570.9350.941000.155
2.055-2.1330.2132280.17332530.17534820.9420.95299.97130.142
2.133-2.220.1851720.16331570.16533300.9510.95799.970.135
2.22-2.3180.1681390.15130460.15131860.9620.96699.96860.125
2.318-2.4310.2031540.15629160.15830700.9480.9641000.131
2.431-2.5620.1681580.14727680.14829260.9630.9691000.129
2.562-2.7170.2151290.15726440.15927730.9430.9631000.14
2.717-2.9040.1931340.16424780.16626120.950.9611000.151
2.904-3.1360.1961120.17823070.17924200.9540.96599.95870.171
3.136-3.4340.2251190.18721510.18922700.9540.9641000.184
3.434-3.8370.193950.16319480.16520430.9650.9711000.165
3.837-4.4250.151030.12917170.1318200.9770.9791000.136
4.425-5.4090.17790.13814870.13915660.9790.9841000.146
5.409-7.6030.213530.18911940.1912470.9750.9721000.195
7.603-48.8680.206420.2056970.2057450.9510.96199.19460.225
Refinement TLS params.Method: refined / Origin x: 37.0918 Å / Origin y: 9.731 Å / Origin z: 16.2676 Å
111213212223313233
T0.0199 Å2-0.0103 Å20.0037 Å2-0.0349 Å20.0022 Å2--0.0059 Å2
L0.273 °2-0.0423 °2-0.0208 °2-0.3974 °20.1274 °2--0.521 °2
S-0.0055 Å °0.0216 Å °0.0334 Å °-0.0396 Å °-0.0178 Å °-0.003 Å °0.039 Å °0.0003 Å °0.0233 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 315
2X-RAY DIFFRACTION1ALLAaA601
3X-RAY DIFFRACTION1ALLAbA602
4X-RAY DIFFRACTION1ALLAcA603
5X-RAY DIFFRACTION1ALLAdA604
6X-RAY DIFFRACTION1ALLAeA605
7X-RAY DIFFRACTION1ALLAfA606
8X-RAY DIFFRACTION1ALLAgA607
9X-RAY DIFFRACTION1ALLAhA608
10X-RAY DIFFRACTION1ALLAiA609
11X-RAY DIFFRACTION1ALLAjA701 - 1030

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