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- PDB-5lf6: Human 20S proteasome complex with Z-LLY-ketoaldehyde at 2.1 Angstrom -

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Basic information

Entry
Database: PDB / ID: 5lf6
TitleHuman 20S proteasome complex with Z-LLY-ketoaldehyde at 2.1 Angstrom
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • LLY-ketoaldehyde peptide
KeywordsHYDROLASE / Proteasome / Multicatalytic Proteinase / NTN-Hydrolase
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / response to organonitrogen compound / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / proteasomal protein catabolic process / P-body / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / lipopolysaccharide binding / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / response to virus / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / response to organic cyclic compound / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / nuclear matrix / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of NF-kappaB transcription factor activity / peptidase activity / ER-Phagosome pathway / regulation of inflammatory response / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / endopeptidase activity / response to oxidative stress / ficolin-1-rich granule lumen / nuclear body / ribosome / Ub-specific processing proteases / cadherin binding / intracellular membrane-bounded organelle / centrosome / synapse / ubiquitin protein ligase binding / Neutrophil degranulation / mitochondrion / proteolysis
Similarity search - Function
Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 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 alpha6 / Proteasome subunit alpha5 ...Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 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 alpha6 / Proteasome subunit alpha5 / 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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / benzyl chlorocarbonate / 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 ...: / benzyl chlorocarbonate / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.07 Å
AuthorsSchrader, J. / Henneberg, F. / Mata, R. / Tittmann, K. / Schneider, T.R. / Stark, H. / Bourenkov, G. / Chari, A.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationCH1098/1-1 Germany
German Research FoundationSFB860-TP A5 Germany
Bundesministerium fuer Bildung und Forschung05K2013-624 Germany
CitationJournal: Science / Year: 2016
Title: The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design.
Authors: Schrader, J. / Henneberg, F. / Mata, R.A. / Tittmann, K. / Schneider, T.R. / Stark, H. / Bourenkov, G. / Chari, A.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
c: LLY-ketoaldehyde peptide
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
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-2
d: LLY-ketoaldehyde peptide
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)724,741112
Polymers719,82830
Non-polymers4,91382
Water63,0713501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area128080 Å2
ΔGint-1109 kcal/mol
Surface area209550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.870, 203.480, 315.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 232
2010O3 - 232
1020B2 - 249
2020P2 - 249
1030C2 - 237
2030Q2 - 237
1040D9 - 241
2040R9 - 241
1050E4 - 236
2050S4 - 236
1060F6 - 243
2060T6 - 243
1070G2 - 245
2070U2 - 245
1080H1 - 220
2080V1 - 220
1090I1 - 204
2090W1 - 204
10100J1 - 196
20100X1 - 196
10110K1 - 199
20110Y1 - 199
10120L1 - 213
20120Z1 - 213
10130M1 - 216
20130a1 - 216
10140N1 - 201
20140b1 - 201

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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Components

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

#1: 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) / Cell line: HELA
References: UniProt: P25787, proteasome endopeptidase complex
#2: 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) / Cell line: HELA
References: UniProt: P25789, proteasome endopeptidase complex
#3: 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 / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: O14818, proteasome endopeptidase complex
#4: 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) / Cell line: HELA
References: UniProt: P28066, proteasome endopeptidase complex
#5: 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: 29720.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P25786, proteasome endopeptidase complex
#6: 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) / Cell line: HELA
References: UniProt: P25788, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-6 / / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27739.760 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P60900, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#8: Protein Proteasome subunit beta type-7 / / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 25321.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: Q99436, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / PSMB3 / 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) / Cell line: HELA
References: UniProt: P49720, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-2 / PSMB2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22989.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P49721, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-5 / PSMB5 / 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: 22484.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28074, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-1 / PSMB1 / 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: 23578.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P20618, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-4 / PSMB4 / 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: 24414.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28070, proteasome endopeptidase complex
#15: 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: 21921.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28072, proteasome endopeptidase complex

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Protein/peptide , 1 types, 2 molecules cd

#11: Protein/peptide LLY-ketoaldehyde peptide


Mass: 423.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 3583 molecules

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


Mass: 35.453 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#18: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Mg
#19: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#20: Chemical ChemComp-PHQ / benzyl chlorocarbonate / Benzyl chloroformate


Mass: 170.593 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H7ClO2
#21: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3501 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.65 %
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
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2015 / Details: CRL Transfocator
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.07→171.02 Å / Num. obs: 403247 / % possible obs: 96.4 % / Redundancy: 6.92 % / CC1/2: 0.99 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.9
Reflection shellResolution: 2.07→2.15 Å / Mean I/σ(I) obs: 0.6 / CC1/2: 0.22 / % possible all: 72.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LE5

5le5


Resolution: 2.07→171.02 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 14.503 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22669 21152 5 %RANDOM
Rwork0.18639 ---
obs0.18839 403247 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.765 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å2-0 Å2-0 Å2
2--1.13 Å2-0 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.07→171.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47957 0 215 3501 51673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01949344
X-RAY DIFFRACTIONr_bond_other_d0.0050.0246892
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.96966756
X-RAY DIFFRACTIONr_angle_other_deg1.2813107642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20556303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04223.7112126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.522158271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.67915340
X-RAY DIFFRACTIONr_chiral_restr0.1060.27541
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0256166
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0211214
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6642.88525033
X-RAY DIFFRACTIONr_mcbond_other1.6642.88525032
X-RAY DIFFRACTIONr_mcangle_it2.7554.31831274
X-RAY DIFFRACTIONr_mcangle_other2.7554.31831275
X-RAY DIFFRACTIONr_scbond_it2.2493.13724311
X-RAY DIFFRACTIONr_scbond_other2.2493.13724311
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4844.59735442
X-RAY DIFFRACTIONr_long_range_B_refined8.99424.41557201
X-RAY DIFFRACTIONr_long_range_B_other8.99424.41657202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A259420.07
12O259420.07
21B278280.08
22P278280.08
31C251300.1
32Q251300.1
41D263520.08
42R263520.08
51E273200.08
52S273200.08
61F280240.08
62T280240.08
71G264300.08
72U264300.08
81H247440.06
82V247440.06
91I256980.07
92W256980.07
101J245120.08
102X245120.08
111K232840.09
112Y232840.09
121L247540.07
122Z247540.07
131M249160.07
132a249160.07
141N229660.06
142b229660.06
LS refinement shellResolution: 2.074→2.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 893 -
Rwork0.402 16897 -
obs--55.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.55220.24110.17510.7489-0.01540.45150.01010.0310.002-0.1218-0.08-0.13160.18790.22370.070.45750.12460.06720.22260.06610.089676.906206.7491.124
20.39790.00970.06030.3775-0.29640.3907-0.03120.0454-0.0593-0.2233-0.036-0.03650.34030.06610.06720.77960.16210.06980.0505-0.01040.050464.861177.803-0.063
31.0043-0.2168-0.03150.19460.04710.25340.0172-0.0172-0.2427-0.08490.0514-0.00320.2301-0.0643-0.06860.9418-0.1026-0.10590.03840.00690.106834.156169.714-3.907
40.3954-0.067-0.21960.9688-0.24170.5370.01060.081-0.0044-0.26450.11770.12910.2981-0.312-0.12830.7092-0.2317-0.21170.2070.08440.070910.365188.598-7.844
50.4469-0.27880.04540.2980.1030.82030.0491-0.0063-0.1503-0.0349-0.01570.06870.1291-0.2754-0.03350.4614-0.0663-0.06390.20880.04630.11649.831219.904-9
60.6129-0.09810.07310.2728-0.05630.29570.0130.02770.0856-0.0353-0.02140.0310.0142-0.01480.00840.46190.0076-0.0280.11040.03920.13832.394240.101-7.584
70.30070.0235-0.05660.66060.18040.26910.05710.07260.0847-0.0915-0.0942-0.04040.01740.11750.03710.45570.01540.02360.17990.08490.127864.017233.587-3.672
80.00880.0162-0.00510.3745-0.26370.39240.0064-0.0065-0.0033-0.045-0.09360.01540.00280.26420.08720.4075-0.00360.03340.24840.06380.114571.352213.93239.439
90.26890.12610.0030.296-0.42760.961-0.0012-0.01630.0106-0.1114-0.09810.00420.20630.23910.09930.50460.10470.04840.17080.04990.089866.571186.51839.549
100.43070.0585-0.25590.1949-0.07131.2045-0.0440.0334-0.0366-0.13670.00360.06690.3738-0.01670.04040.6561-0.012-0.02260.01130.00650.101439.129170.26536.27
110.1724-0.019-0.19790.58590.09141.04060.03710.0306-0.0056-0.15030.10630.07540.3082-0.279-0.14340.5206-0.2185-0.12910.19190.12040.1288.034180.78332.228
120.16560.0635-0.17390.44750.09390.69850.0265-0.00410.0013-0.1160.15640.07820.0364-0.3027-0.18290.3602-0.0865-0.08580.36260.19380.1312-1.575210.26930.853
130.1244-0.0254-0.11290.2149-0.21190.8443-0.00410.02550.0130.0310.13810.0298-0.1575-0.1786-0.1340.43980.06490.01560.19450.07560.145716.302237.92133.116
140.3007-0.0135-0.05150.2961-0.2220.88740.03880.05570.00420.0436-0.03560.0096-0.17150.0645-0.00320.4949-0.0480.00570.09590.01950.120248.774241.43535.653
150.38270.17670.12021.17830.18940.43860.0325-0.07940.06110.12970.04090.296-0.2227-0.2936-0.07330.42140.2550.20820.36450.14250.1544-7.241225.984103.023
160.0886-0.02570.05140.74110.14720.4118-0.0076-0.0329-0.03040.12440.14430.2018-0.0106-0.3029-0.13670.3261-0.01310.12760.44710.23330.1867-8.101194.56104.928
171.4203-0.05140.19470.18720.110.53240.0978-0.0123-0.37150.11210.08320.0360.1404-0.1542-0.18110.4811-0.0717-0.00720.1730.09840.208515.779174.605109.611
180.4192-0.1667-0.07810.2747-0.21910.6483-0.064-0.0466-0.0621-0.01850.06990.03810.11570.0882-0.00580.46090.00820.04330.15990.04180.097245.947181.837112.775
190.3875-0.08560.08750.4307-0.29450.7279-0.0174-0.0692-0.04570.1017-0.0607-0.0093-0.18130.2860.07810.4782-0.08340.00420.25140.02630.052459.071210.3113.839
201.00920.0362-0.25140.3170.01920.56370.0997-0.17460.04590.077-0.03710.0284-0.46820.0627-0.06260.7893-0.09510.08140.0707-0.04050.031846.67237.872111.409
210.77340.1629-0.06110.3664-0.00440.09680.003-0.13910.14840.0950.01690.0334-0.2062-0.1006-0.01990.81410.23890.15350.1722-0.01640.093616.234244.623107.391
220.16950.24010.05740.55340.09120.39620.02120.01990.00760.07260.13580.0707-0.2079-0.3205-0.1570.42230.17350.11210.35490.16440.15361.183230.24364.989
230.086-0.11220.02840.49530.28871.33250.0271-0.03120.01230.04030.18030.04670.0247-0.4457-0.20740.2897-0.02740.03160.43030.22260.1696-6.21202.94565.087
240.2238-0.0264-0.15510.3951-0.03580.8638-0.0292-0.04410.0159-0.02880.09980.04190.2276-0.1623-0.07060.4371-0.1416-0.02490.17020.09890.152111.65176.66968.738
250.45050.1578-0.19720.4627-0.15310.98680.0198-0.08750.0327-0.046-0.03220.01160.2350.06680.01240.50610.01460.00330.0940.03340.144.164172.95772.716
260.1608-0.141-0.12610.4193-0.21450.62160.0353-0.03640.01060.0127-0.1060.0230.0340.22530.07080.41880.0060.00520.23510.05020.110865.429195.82673.767
270.2015-0.0439-0.09490.2138-0.24850.91040.0057-0.0263-0.00180.1084-0.0520.0299-0.22180.19520.04630.4818-0.0979-0.00870.16650.00930.09160.635228.53470.965
280.25090.01150.0020.2839-0.16011.05690.0021-0.0214-0.00990.1070.03890.037-0.3229-0.0803-0.0410.60330.0460.05530.0461-0.00680.089232.669245.35467.969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 232
2X-RAY DIFFRACTION2B2 - 249
3X-RAY DIFFRACTION3C2 - 238
4X-RAY DIFFRACTION4D9 - 241
5X-RAY DIFFRACTION5E4 - 237
6X-RAY DIFFRACTION6F6 - 244
7X-RAY DIFFRACTION7G2 - 245
8X-RAY DIFFRACTION8H1 - 220
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 196
11X-RAY DIFFRACTION11K1 - 200
12X-RAY DIFFRACTION12L1 - 213
13X-RAY DIFFRACTION13M1 - 216
14X-RAY DIFFRACTION14N1 - 202
15X-RAY DIFFRACTION15O3 - 232
16X-RAY DIFFRACTION16P2 - 248
17X-RAY DIFFRACTION17Q2 - 240
18X-RAY DIFFRACTION18R9 - 241
19X-RAY DIFFRACTION19S4 - 239
20X-RAY DIFFRACTION20T5 - 244
21X-RAY DIFFRACTION21U2 - 245
22X-RAY DIFFRACTION22V1 - 220
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 196
25X-RAY DIFFRACTION25Y1 - 199
26X-RAY DIFFRACTION26Z1 - 213
27X-RAY DIFFRACTION27a1 - 216
28X-RAY DIFFRACTION28b1 - 203

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