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- PDB-8bzl: Human 20S Proteasome in complex with peptide activator peptide BLM42 -

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Basic information

Entry
Database: PDB / ID: 8bzl
TitleHuman 20S Proteasome in complex with peptide activator peptide BLM42
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • ARG-SER-TYR-TYR-SER
KeywordsHYDROLASE / activator peptide / 20S proteasome / protein degradation / threonine protease
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / negative regulation of inflammatory response to antigenic stimulus / P-body / Degradation of AXIN / lipopolysaccharide binding / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / G2/M Checkpoints / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / response to virus / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / nuclear matrix / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / peptidase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / response to oxidative stress / regulation of inflammatory response / secretory granule lumen / endopeptidase activity / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / nuclear body / cilium / ciliary basal body / cadherin binding / ribosome / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / Neutrophil degranulation / centrosome / mitochondrion / proteolysis / RNA binding / extracellular exosome / extracellular region
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit ...Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
: / 1-ETHYL-PYRROLIDINE-2,5-DIONE / Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 ...: / 1-ETHYL-PYRROLIDINE-2,5-DIONE / Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsHenneberg, F. / Chari, A. / Jankowska, E. / Witkowska, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Blm10-Based Compounds Add to the Knowledge of How Allosteric Modulators Influence Human 20S Proteasome.
Authors: Witkowska, J. / Gizynska, M. / Karpowicz, P. / Sowik, D. / Trepczyk, K. / Hennenberg, F. / Chari, A. / Gieldon, A. / Pierzynowska, K. / Gaffke, L. / Wegrzyn, G. / Jankowska, E.
History
DepositionDec 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 2.0Feb 26, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / struct_asym / struct_conn / struct_ncs_dom / struct_ncs_dom_lim
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.pdbx_tls_group_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: Proteasome subunit beta type-3
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
H: Proteasome subunit beta type-7
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-2
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-1
M: Proteasome subunit beta type-4
N: Proteasome subunit beta type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit alpha type-6
V: Proteasome subunit beta type-7
X: Proteasome subunit beta type-2
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-6
c: ARG-SER-TYR-TYR-SER
d: ARG-SER-TYR-TYR-SER
e: ARG-SER-TYR-TYR-SER
f: ARG-SER-TYR-TYR-SER
g: ARG-SER-TYR-TYR-SER
h: ARG-SER-TYR-TYR-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)777,610117
Polymers772,56534
Non-polymers5,04583
Water61,7193426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area128060 Å2
ΔGint-1125 kcal/mol
Surface area205730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.915, 203.262, 316.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
113
21I
32A
42O
53B
63P
74C
84Q
95D
105R
116E
126S
137F
147T
158G
168U
179H
189V
1910J
2010X
2111K
2211Y
2312L
2412Z
2513M
2613a
2714N
2814b

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERASPASP3A1 - 2042 - 205
211SERSERASPASPIJ1 - 2042 - 205
322ARGARGLEULEUAB3 - 2294 - 230
422ARGARGLEULEUOP3 - 2294 - 230
533SERSERGLUGLUBC2 - 2432 - 243
633SERSERGLUGLUPQ2 - 2432 - 243
744SERSERVALVALCD2 - 2292 - 229
844SERSERVALVALQR2 - 2292 - 229
955ASPASPILEILEDE9 - 2389 - 238
1055ASPASPILEILERS9 - 2389 - 238
1166ASNASNLEULEUEF4 - 2364 - 236
1266ASNASNLEULEUST4 - 2364 - 236
1377GLYGLYLEULEUFG6 - 2437 - 244
1477GLYGLYLEULEUTU6 - 2437 - 244
1588GLYGLYALAALAGH4 - 2434 - 243
1688GLYGLYALAALAUV4 - 2434 - 243
1799THRTHRGLUGLUHI1 - 22044 - 263
1899THRTHRGLUGLUVW1 - 22044 - 263
191010METMETPHEPHEJK1 - 1961 - 196
201010METMETPHEPHEXX1 - 1961 - 196
211111THRTHRLYSLYSKL1 - 19860 - 257
221111THRTHRLYSLYSYY1 - 19860 - 257
231212ARGARGASPASPLM1 - 21329 - 241
241212ARGARGASPASPZZ1 - 21329 - 241
251313THRTHRHISHISMN1 - 21346 - 258
261313THRTHRHISHISaAA1 - 21346 - 258
271414THRTHRLYSLYSNO1 - 19635 - 230
281414THRTHRLYSLYSbBA1 - 19635 - 230

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28

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Components

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Proteasome subunit beta type- ... , 7 types, 14 molecules 3IHVJXKYLZMaNb

#1: Protein Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22972.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P49720, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 30000.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The structure shows the processed mature form of the sequence.
Source: (natural) Homo sapiens (human)
References: UniProt: Q99436, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22864.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Modified cysteine residue / Source: (natural) Homo sapiens (human)
References: UniProt: P49721, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


Mass: 28510.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The structure shows the processed mature form of the sequence.
Source: (natural) Homo sapiens (human)
References: UniProt: P28074, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 26522.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P20618, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex ...26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 29231.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28070, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-6 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 25377.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28072, proteasome endopeptidase complex

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Proteasome subunit alpha type- ... , 7 types, 14 molecules AOBPCQDRESFTGU

#2: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25787
#3: Protein Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25789
#4: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27986.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Modified cysteine residue / Source: (natural) Homo sapiens (human) / References: UniProt: O14818
#5: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P28066
#6: Protein Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29595.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Modified cysteine residue / Source: (natural) Homo sapiens (human) / References: UniProt: P25786
#7: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25788
#8: Protein Proteasome subunit alpha type-6 / 27 kDa prosomal protein / PROS-27 / p27K / Macropain iota chain / Multicatalytic endopeptidase ...27 kDa prosomal protein / PROS-27 / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain / Proteasome subunit alpha-1 / alpha-1


Mass: 27489.510 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: modified cysteine residue / Source: (natural) Homo sapiens (human) / References: UniProt: P60900

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Protein/peptide , 1 types, 6 molecules cdefgh

#15: Protein/peptide
ARG-SER-TYR-TYR-SER


Mass: 1790.950 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 3509 molecules

#16: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#18: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#19: Chemical
ChemComp-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H9NO2
#20: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3426 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.14→107.181 Å / Num. obs: 327921 / % possible obs: 94.5 % / Redundancy: 7.1 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.995 / CC1/2 anomalous: -0.256 / Rmerge(I) obs: 0.1366 / Rpim(I) all: 0.055 / Rrim(I) all: 0.1474 / AbsDiff over sigma anomalous: 0.585 / Baniso tensor eigenvalue 1: 22.7677 Å2 / Baniso tensor eigenvalue 2: 3.451 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.395 Å / Aniso diffraction limit 2: 2.14 Å / Aniso diffraction limit 3: 2.248 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 6.65 / Num. measured all: 2327154 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 94.5 / % possible ellipsoidal: 94.5 / % possible ellipsoidal anomalous: 94.5 / % possible spherical: 81.6 / % possible spherical anomalous: 81.2 / Redundancy anomalous: 3.65 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
6.313-107.1816.960.06312.4111419611419616396163960.996-0.2520.02570.06820.27510099.810099.81003.7699.8
4.987-6.3136.940.078912.0211382411382416395163950.995-0.4390.03220.08540.39999.810099.810099.83.64100
4.346-4.9877.040.097412.2111537211537216397163970.992-0.430.03920.10510.46299.799.899.799.899.73.6699.8
3.941-4.3467.130.104511.9211687111687116396163960.99-0.3090.04170.11270.46799.399.799.399.799.33.799.7
3.655-3.9417.170.100811.3911762311762316395163950.993-0.1890.04030.10870.47299.799.999.799.999.73.7199.9
3.437-3.6557.210.117410.7411813411813416395163950.991-0.2080.04690.12660.52199.910099.910099.93.71100
3.263-3.4377.10.1449.6311636111636116398163980.99-0.2880.0580.15540.5691001001001001003.65100
3.119-3.2636.860.17218.3411247411247416395163950.986-0.2170.07070.18630.62499.910099.910099.93.53100
2.998-3.1196.850.19727.2411236011236016395163950.982-0.1790.08080.21340.66399.610099.610099.63.52100
2.893-2.9986.910.22826.3911334811334816400164000.981-0.1540.09290.24660.65999.699.999.699.999.63.5599.9
2.802-2.8936.960.2765.5211405311405316396163960.975-0.1260.1120.29820.67499.699.999.699.999.63.5799.9
2.72-2.8026.980.33514.6711446811446816394163940.965-0.0490.13560.36180.67298.899.198.899.198.83.5799.1
2.646-2.727.060.40964.0911572011572016397163970.95-0.0370.16510.4420.69897.497.497.497.497.43.697.4
2.579-2.6467.120.47683.5811668511668516393163930.941-0.0260.19140.51420.67796.296.196.296.196.23.6396.1
2.517-2.5797.150.59062.9711729111729116396163960.91-0.0270.23680.63680.64995.395.195.395.195.33.6595.1
2.46-2.5177.20.68182.6211798511798516397163970.882-0.0180.27270.73480.64394.293.894.293.894.23.6793.8
2.407-2.467.220.86722.1911837111837116397163970.8330.0170.34620.93440.6692.692.292.692.292.63.6892.2
2.355-2.4077.310.98971.8911990011990016398163980.794-0.0140.39261.06550.61589.489.189.487.287.53.7389.1
2.295-2.3557.351.16721.6712057012057016394163940.72-0.0020.46151.2560.62679.980.279.968.2683.7680.2
2.14-2.2957.411.41841.5312154812154816397163970.635-0.0120.55851.52540.62363.762.963.721.721.63.7962.9
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROC1.0.5 20220608data processing
XDSJan 10, 2022data reduction
Aimless0.7.8data scaling
Coot0.9.8.2model building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→107.123 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.216 / SU B: 13.54 / SU ML: 0.172 / Average fsc free: 0.9609 / Average fsc work: 0.9696 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.213 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 16354 4.987 %RANDOM
Rwork0.1962 311565 --
all0.198 ---
obs-327919 81.566 %-
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: 47.647 Å2
Baniso -1Baniso -2Baniso -3
1--0.295 Å2-0 Å20 Å2
2--0.477 Å2-0 Å2
3----0.182 Å2
Refinement stepCycle: LAST / Resolution: 2.14→107.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47032 0 236 3404 50672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01248329
X-RAY DIFFRACTIONr_angle_refined_deg0.8921.64765442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11856187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.525.118338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.254108026
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.107102038
X-RAY DIFFRACTIONr_chiral_restr0.0740.27415
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0235935
X-RAY DIFFRACTIONr_nbd_refined0.1930.221627
X-RAY DIFFRACTIONr_nbtor_refined0.2960.233299
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.22873
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.212
X-RAY DIFFRACTIONr_mcbond_it0.662.05424682
X-RAY DIFFRACTIONr_mcangle_it1.1883.07330798
X-RAY DIFFRACTIONr_scbond_it0.8262.16423647
X-RAY DIFFRACTIONr_scangle_it1.3713.19734613
X-RAY DIFFRACTIONr_lrange_it6.9131.62373080
X-RAY DIFFRACTIONr_ncsr_local_group_10.0550.056372
X-RAY DIFFRACTIONr_ncsr_local_group_20.050.056305
X-RAY DIFFRACTIONr_ncsr_local_group_30.050.056914
X-RAY DIFFRACTIONr_ncsr_local_group_40.0820.056389
X-RAY DIFFRACTIONr_ncsr_local_group_50.0490.056469
X-RAY DIFFRACTIONr_ncsr_local_group_60.0510.057079
X-RAY DIFFRACTIONr_ncsr_local_group_70.0620.057370
X-RAY DIFFRACTIONr_ncsr_local_group_80.0660.056944
X-RAY DIFFRACTIONr_ncsr_local_group_90.0610.056597
X-RAY DIFFRACTIONr_ncsr_local_group_100.0460.056417
X-RAY DIFFRACTIONr_ncsr_local_group_110.0420.056277
X-RAY DIFFRACTIONr_ncsr_local_group_120.0430.056612
X-RAY DIFFRACTIONr_ncsr_local_group_130.0410.056794
X-RAY DIFFRACTIONr_ncsr_local_group_140.020.056068
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
113X-RAY DIFFRACTIONLocal ncs0.054660.05011
123X-RAY DIFFRACTIONLocal ncs0.054660.05011
233X-RAY DIFFRACTIONLocal ncs0.049640.0501
243X-RAY DIFFRACTIONLocal ncs0.049640.0501
353X-RAY DIFFRACTIONLocal ncs0.050060.05011
363X-RAY DIFFRACTIONLocal ncs0.050060.05011
473X-RAY DIFFRACTIONLocal ncs0.081660.05011
483X-RAY DIFFRACTIONLocal ncs0.081660.05011
593X-RAY DIFFRACTIONLocal ncs0.048830.05011
5103X-RAY DIFFRACTIONLocal ncs0.048830.05011
6113X-RAY DIFFRACTIONLocal ncs0.051250.05011
6123X-RAY DIFFRACTIONLocal ncs0.051250.05011
7133X-RAY DIFFRACTIONLocal ncs0.06210.05011
7143X-RAY DIFFRACTIONLocal ncs0.06210.05011
8153X-RAY DIFFRACTIONLocal ncs0.066280.0501
8163X-RAY DIFFRACTIONLocal ncs0.066280.0501
9173X-RAY DIFFRACTIONLocal ncs0.061240.0501
9183X-RAY DIFFRACTIONLocal ncs0.061240.0501
10193X-RAY DIFFRACTIONLocal ncs0.045630.05011
10203X-RAY DIFFRACTIONLocal ncs0.045630.05011
11213X-RAY DIFFRACTIONLocal ncs0.042340.05011
11223X-RAY DIFFRACTIONLocal ncs0.042340.05011
12233X-RAY DIFFRACTIONLocal ncs0.042850.0501
12243X-RAY DIFFRACTIONLocal ncs0.042850.0501
13253X-RAY DIFFRACTIONLocal ncs0.04060.05011
13263X-RAY DIFFRACTIONLocal ncs0.04060.05011
14273X-RAY DIFFRACTIONLocal ncs0.019990.05011
14283X-RAY DIFFRACTIONLocal ncs0.019990.05011
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
2.14-2.1960.2951070.28622400.287294950.9430.9437.95730.289
2.196-2.2560.3113090.29158320.292287560.9340.94221.35550.292
2.256-2.3210.3037470.294136460.294279890.9370.94251.42380.293
2.321-2.3920.29610630.277206760.278271510.9430.9580.0670.273
2.392-2.4710.28512220.262230470.263264120.9450.95591.88630.256
2.471-2.5580.26212070.242228590.243254720.9550.96294.48020.233
2.558-2.6540.26711610.223225120.225246810.9540.96895.91590.212
2.654-2.7620.25311140.218220810.219236940.9580.9797.8940.207
2.762-2.8850.25411650.214215440.216227410.9590.97199.85930.204
2.885-3.0260.24611130.208207120.21218450.960.97399.90840.203
3.026-3.1890.22810860.198196390.2207250.9680.9761000.2
3.189-3.3830.22710050.189186860.191196910.970.9791000.198
3.383-3.6160.219720.183175110.184184830.9750.9821000.199
3.616-3.9050.2168570.174164020.176172810.9740.98399.87270.197
3.905-4.2770.1967830.168150690.17158900.9770.98399.76090.199
4.277-4.7810.1857000.16137110.161144600.9790.98499.66110.201
4.781-5.5190.2136220.171121710.173128000.9730.98299.94530.22
5.519-6.7550.2344800.21104260.211109060.970.9751000.266
6.755-9.5340.1844100.16981310.1785410.9830.9851000.23
9.534-107.1230.2112310.21346690.21349350.9710.96899.29080.302
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)
11.39590.43540.49842.0105-0.13761.9961-0.00940.14480.05-0.2806-0.1023-0.42920.15550.59210.11170.23120.13420.12910.27740.06450.20976.3296206.35471.1938
21.2519-0.24090.06681.8224-0.21271.1223-0.05010.3009-0.1184-0.3623-0.0482-0.32210.36660.35480.09830.59240.11140.06880.1821-0.0310.209862.794178.27450.4845
32.01040.0566-0.04053.0502-0.1411.8963-0.08490.0306-0.4869-0.27130.0828-0.02020.5278-0.05520.00210.6344-0.1229-0.11210.2328-0.0150.269332.7551170.8208-3.2512
40.176-0.1297-0.4030.6630.10081.2548-0.00510.1863-0.134-0.2877-0.06110.13560.2096-0.40020.06630.5353-0.162-0.23340.59580.02680.40998.8943189.2794-7.0666
52.09020.11440.34210.8097-0.11721.47680.03150.1627-0.2725-0.22250.06870.27060.2083-0.4861-0.10010.2595-0.1323-0.19290.29490.11340.27549.7322220.9804-8.7179
61.8698-0.77460.00171.6484-0.13831.27630.03910.14380.1853-0.1988-0.05910.1276-0.0663-0.14770.020.1195-0.0401-0.09050.0920.1020.1932.5809240.5121-7.658
70.89550.08820.13112.06780.39011.18890.00790.23940.1994-0.402-0.0593-0.1608-0.07950.31820.05140.141-0.00550.05640.19940.13490.179263.9215233.4074-3.5982
80.11620.0123-0.0641.9906-0.21740.8104-0.0076-0.0176-0.12010.125-0.0984-0.1950.08380.36530.1060.06890.00130.01430.21860.06210.198271.4185213.981939.5416
90.61920.19250.66561.1231-0.78081.93050.04890.0625-0.0316-0.0895-0.1434-0.09270.15580.40380.09440.18050.07620.03080.15680.05430.144466.0294186.602539.8004
101.08020.68290.08730.9537-0.49752.6402-0.05510.0794-0.0221-0.20690.03640.19010.513-0.17540.01870.3636-0.0339-0.05360.0341-0.00390.171438.2087170.408936.6901
111.2296-0.0274-0.82491.3666-0.12852.159-0.03340.1915-0.0317-0.20420.04490.19760.3643-0.3889-0.01150.2252-0.2107-0.1470.24160.11740.27417.1058181.60432.8384
121.07960.0593-0.55311.36420.41641.21750.024-0.03630.1312-0.12060.03330.3442-0.0245-0.4743-0.05730.0756-0.0858-0.09720.40790.19080.3513-1.9011211.292531.1523
131.33540.30210.14131.25130.25741.9398-0.0348-0.01350.21150.05510.09550.245-0.3344-0.3213-0.06070.08290.06110.02060.15810.13930.263916.5752238.53132.9165
141.3408-0.3750.29240.97460.17782.79430.04560.02950.07950.0137-0.05880.0072-0.36210.19340.01330.1222-0.06520.01260.04780.03080.141548.9393241.510334.9413
150.8956-0.1620.39931.2381-0.13391.8724-0.0282-0.11390.18180.14970.00250.368-0.3262-0.48540.02580.33540.09010.2750.49210.03410.4533-6.2239226.305103.1502
161.39990.40930.12451.27450.23091.079-0.0337-0.240.05870.21550.02980.3777-0.0632-0.520.00380.2595-0.04580.230.50440.10910.4058-7.0315196.1624104.9976
172.37230.1309-0.1422.18250.09051.99870.03640.0065-0.46090.1446-0.00090.33960.4418-0.3269-0.03550.4075-0.09140.11380.31030.12070.331516.4031176.7283109.1384
180.53610.3458-0.29081.11650.14761.6618-0.1147-0.1925-0.13060.39010.07460.14960.166-0.00950.04010.44010.03790.08110.26210.0990.232745.5751182.0188113.116
191.2992-0.66240.29861.5965-0.33721.6552-0.0157-0.3025-0.13010.26480.024-0.10160.01150.2944-0.00830.4083-0.1583-0.0460.24490.04550.144559.1112210.5579114.2034
202.22880.31540.12191.30350.21161.04460.124-0.34760.16440.207-0.103-0.1531-0.34810.1704-0.02110.6035-0.12930.08210.1696-0.04770.165447.4902238.5728111.4673
211.18650.3406-0.12461.3961-0.18650.8969-0.0001-0.24450.34210.325-0.04120.138-0.4339-0.19090.04130.61460.09160.21450.2981-0.07650.36817.2447245.2205107.3774
220.70360.550.07771.3951-0.18890.56920.00230.020.04560.08450.08930.2951-0.1927-0.3749-0.09160.20410.10470.17860.36570.08370.37991.3619231.604265.4797
230.62970.02580.76521.11030.46141.57670.0013-0.07440.0658-0.01680.05660.2796-0.1182-0.4349-0.05780.1082-0.03930.09570.45540.16410.4154-6.3869204.309465.6301
240.5634-0.25580.10680.8370.33962.3727-0.0462-0.0929-0.060.04340.10680.08130.4079-0.1592-0.06060.2073-0.15060.00230.1910.0990.288710.8112177.56569.3041
251.37770.1318-0.57071.37840.16642.1463-0.0243-0.18280.01040.1136-0.023-0.00440.39660.06090.04730.2157-0.0086-0.02810.03050.02560.128143.5053173.269173.1333
260.8754-0.0586-0.44421.6498-0.08461.48810.0396-0.03030.0260.0817-0.1342-0.23110.07950.42660.09460.0954-0.0116-0.0160.15840.06020.149565.2271195.827974.1044
271.3035-0.1704-0.11721.5956-0.45831.63790.02180.01160.11830.1622-0.0928-0.169-0.28370.29370.0710.1805-0.1199-0.00080.09190.00790.124660.9405228.552771.3873
281.6498-0.03110.0160.95760.02671.97140.016-0.02460.11250.245-0.01290.1699-0.4225-0.1213-0.00310.30270.02680.08750.04730.00740.184333.2309245.825968.8885
297.983-9.847-1.728712.6283.46954.1507-0.05250.0187-0.0577-0.04940.09680.0448-0.27030.1878-0.04420.283-0.04360.04350.34680.01150.30776.4178188.6707116.2545
304.8736-2.8675-1.90221.68821.11980.7436-0.00840.1586-0.1350.0092-0.0660.07660.0163-0.0490.07450.3873-0.0082-0.02450.30520.00430.375447.0468177.0476-10.8326
316.83427.7103-3.00949.4318-3.96592.1438-0.21690.1756-0.33620.13840.3683-0.00870.11640.0022-0.15150.5740.1330.13720.4516-0.02460.5302-5.128209.1819113.6098
329.2907-10.7059-0.323113.844-1.27171.8597-0.3781-0.74990.15910.14260.5212-0.04810.20320.5106-0.14310.3703-0.1214-0.02590.4731-0.01810.411714.183207.1582-15.0754
Refinement TLS groupSelection: ALL

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