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- PDB-5w18: Staphylococcus aureus ClpP in complex with (S)-N-((2R,6S,8aS,14aS... -

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Basic information

Entry
Database: PDB / ID: 5w18
TitleStaphylococcus aureus ClpP in complex with (S)-N-((2R,6S,8aS,14aS,20S,23aS)-2,6-dimethyl-5,8,14,19,23-pentaoxooctadecahydro-1H,5H,14H,19H-pyrido[2,1-i]dipyrrolo[2,1-c:2',1'-l][1]oxa[4,7,10,13]tetraazacyclohexadecin-20-yl)-3-phenyl-2-(3-phenylureido)propanamide
Components
  • 9V7-PHE-SER-PRO-YCP-ALA-MP8
  • ATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE/ANTIBIOTIC / ClpP / HYDROLASE-ANTIBIOTIC complex / UDEP
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsLee, R.E. / Griffith, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI110578-04 United States
Citation
Journal: Acs Infect Dis. / Year: 2019
Title: Ureadepsipeptides as ClpP Activators.
Authors: Griffith, E.C. / Zhao, Y. / Singh, A.P. / Conlon, B.P. / Tangallapally, R. / Shadrick, W.R. / Liu, J. / Wallace, M.J. / Yang, L. / Elmore, J.M. / Li, Y. / Zheng, Z. / Miller, D.J. / ...Authors: Griffith, E.C. / Zhao, Y. / Singh, A.P. / Conlon, B.P. / Tangallapally, R. / Shadrick, W.R. / Liu, J. / Wallace, M.J. / Yang, L. / Elmore, J.M. / Li, Y. / Zheng, Z. / Miller, D.J. / Cheramie, M.N. / Lee, R.B. / LaFleur, M.D. / Lewis, K. / Lee, R.E.
#1: Journal: J. Biol. Chem. / Year: 2011
Title: Structural switching of Staphylococcus aureus Clp protease: a key to understanding protease dynamics.
Authors: Zhang, J. / Ye, F. / Lan, L. / Jiang, H. / Luo, C. / Yang, C.G.
#2: Journal: Chem. Biol. / Year: 2010
Title: Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP.
Authors: Li, D.H. / Chung, Y.S. / Gloyd, M. / Joseph, E. / Ghirlando, R. / Wright, G.D. / Cheng, Y.Q. / Maurizi, M.R. / Guarne, A. / Ortega, J.
#3: Journal: J. Biol. Chem. / Year: 2012
Title: Insights into structural network responsible for oligomerization and activity of bacterial virulence regulator caseinolytic protease P (ClpP) protein.
Authors: Gersch, M. / List, A. / Groll, M. / Sieber, S.A.
History
DepositionJun 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.2Nov 6, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
H: 9V7-PHE-SER-PRO-YCP-ALA-MP8
J: 9V7-PHE-SER-PRO-YCP-ALA-MP8
O: 9V7-PHE-SER-PRO-YCP-ALA-MP8
P: 9V7-PHE-SER-PRO-YCP-ALA-MP8
Q: 9V7-PHE-SER-PRO-YCP-ALA-MP8
R: 9V7-PHE-SER-PRO-YCP-ALA-MP8
U: 9V7-PHE-SER-PRO-YCP-ALA-MP8
V: 9V7-PHE-SER-PRO-YCP-ALA-MP8
X: 9V7-PHE-SER-PRO-YCP-ALA-MP8
Y: 9V7-PHE-SER-PRO-YCP-ALA-MP8
Z: 9V7-PHE-SER-PRO-YCP-ALA-MP8
a: 9V7-PHE-SER-PRO-YCP-ALA-MP8
b: 9V7-PHE-SER-PRO-YCP-ALA-MP8
c: 9V7-PHE-SER-PRO-YCP-ALA-MP8


Theoretical massNumber of molelcules
Total (without water)327,17428
Polymers327,17428
Non-polymers00
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60610 Å2
ΔGint-304 kcal/mol
Surface area87460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.923, 126.376, 146.057
Angle α, β, γ (deg.)90.000, 93.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27I
18A
28K
19A
29L
110A
210M
111A
211N
112A
212S
113A
213T
114B
214C
115B
215D
116B
216E
117B
217F
118B
218G
119B
219I
120B
220K
121B
221L
122B
222M
123B
223N
124B
224S
125B
225T
126C
226D
127C
227E
128C
228F
129C
229G
130C
230I
131C
231K
132C
232L
133C
233M
134C
234N
135C
235S
136C
236T
137D
237E
138D
238F
139D
239G
140D
240I
141D
241K
142D
242L
143D
243M
144D
244N
145D
245S
146D
246T
147E
247F
148E
248G
149E
249I
150E
250K
151E
251L
152E
252M
153E
253N
154E
254S
155E
255T
156F
256G
157F
257I
158F
258K
159F
259L
160F
260M
161F
261N
162F
262S
163F
263T
164G
264I
165G
265K
166G
266L
167G
267M
168G
268N
169G
269S
170G
270T
171I
271K
172I
272L
173I
273M
174I
274N
175I
275S
176I
276T
177K
277L
178K
278M
179K
279N
180K
280S
181K
281T
182L
282M
183L
283N
184L
284S
185L
285T
186M
286N
187M
287S
188M
288T
189N
289S
190N
290T
191S
291T

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEVALVALAA4 - 1914 - 191
21ILEILEVALVALBB4 - 1914 - 191
12ILEILEPROPROAA4 - 1924 - 192
22ILEILEPROPROCC4 - 1924 - 192
13ILEILEVALVALAA4 - 1914 - 191
23ILEILEVALVALDD4 - 1914 - 191
14PROPROVALVALAA5 - 1915 - 191
24PROPROVALVALEE5 - 1915 - 191
15ILEILEPROPROAA4 - 1924 - 192
25ILEILEPROPROFF4 - 1924 - 192
16ILEILEVALVALAA4 - 1914 - 191
26ILEILEVALVALGG4 - 1914 - 191
17ILEILEPROPROAA4 - 1924 - 192
27ILEILEPROPROIH4 - 1924 - 192
18ILEILEVALVALAA4 - 1914 - 191
28ILEILEVALVALKI4 - 1914 - 191
19ILEILEVALVALAA4 - 1914 - 191
29ILEILEVALVALLJ4 - 1914 - 191
110ILEILEPROPROAA4 - 1924 - 192
210ILEILEPROPROMK4 - 1924 - 192
111ILEILEPROPROAA4 - 1924 - 192
211ILEILEPROPRONL4 - 1924 - 192
112ILEILEPROPROAA4 - 1924 - 192
212ILEILEPROPROSM4 - 1924 - 192
113ILEILEPROPROAA4 - 1924 - 192
213ILEILEPROPROTN4 - 1924 - 192
114ILEILEVALVALBB4 - 1914 - 191
214ILEILEVALVALCC4 - 1914 - 191
115ILEILEGLUGLUBB4 - 1934 - 193
215ILEILEGLUGLUDD4 - 1934 - 193
116PROPROVALVALBB5 - 1915 - 191
216PROPROVALVALEE5 - 1915 - 191
117ILEILEVALVALBB4 - 1914 - 191
217ILEILEVALVALFF4 - 1914 - 191
118ILEILEGLUGLUBB4 - 1934 - 193
218ILEILEGLUGLUGG4 - 1934 - 193
119ILEILEGLUGLUBB4 - 1934 - 193
219ILEILEGLUGLUIH4 - 1934 - 193
120ILEILEGLUGLUBB4 - 1934 - 193
220ILEILEGLUGLUKI4 - 1934 - 193
121ILEILEGLUGLUBB4 - 1934 - 193
221ILEILEGLUGLULJ4 - 1934 - 193
122ILEILEVALVALBB4 - 1914 - 191
222ILEILEVALVALMK4 - 1914 - 191
123ILEILEVALVALBB4 - 1914 - 191
223ILEILEVALVALNL4 - 1914 - 191
124ILEILEPROPROBB4 - 1924 - 192
224ILEILEPROPROSM4 - 1924 - 192
125ILEILEPROPROBB4 - 1924 - 192
225ILEILEPROPROTN4 - 1924 - 192
126ILEILEVALVALCC4 - 1914 - 191
226ILEILEVALVALDD4 - 1914 - 191
127PROPROVALVALCC5 - 1915 - 191
227PROPROVALVALEE5 - 1915 - 191
128ILEILEPROPROCC4 - 1924 - 192
228ILEILEPROPROFF4 - 1924 - 192
129ILEILEVALVALCC4 - 1914 - 191
229ILEILEVALVALGG4 - 1914 - 191
130ILEILEPROPROCC4 - 1924 - 192
230ILEILEPROPROIH4 - 1924 - 192
131ILEILEVALVALCC4 - 1914 - 191
231ILEILEVALVALKI4 - 1914 - 191
132ILEILEVALVALCC4 - 1914 - 191
232ILEILEVALVALLJ4 - 1914 - 191
133ILEILEPROPROCC4 - 1924 - 192
233ILEILEPROPROMK4 - 1924 - 192
134ILEILEPROPROCC4 - 1924 - 192
234ILEILEPROPRONL4 - 1924 - 192
135ILEILEPROPROCC4 - 1924 - 192
235ILEILEPROPROSM4 - 1924 - 192
136ILEILEPROPROCC4 - 1924 - 192
236ILEILEPROPROTN4 - 1924 - 192
137PROPROVALVALDD5 - 1915 - 191
237PROPROVALVALEE5 - 1915 - 191
138ILEILEVALVALDD4 - 1914 - 191
238ILEILEVALVALFF4 - 1914 - 191
139ILEILEGLUGLUDD4 - 1934 - 193
239ILEILEGLUGLUGG4 - 1934 - 193
140ILEILEGLUGLUDD4 - 1934 - 193
240ILEILEGLUGLUIH4 - 1934 - 193
141ILEILEGLUGLUDD4 - 1934 - 193
241ILEILEGLUGLUKI4 - 1934 - 193
142ILEILEGLUGLUDD4 - 1934 - 193
242ILEILEGLUGLULJ4 - 1934 - 193
143ILEILEVALVALDD4 - 1914 - 191
243ILEILEVALVALMK4 - 1914 - 191
144ILEILEVALVALDD4 - 1914 - 191
244ILEILEVALVALNL4 - 1914 - 191
145ILEILEPROPRODD4 - 1924 - 192
245ILEILEPROPROSM4 - 1924 - 192
146ILEILEPROPRODD4 - 1924 - 192
246ILEILEPROPROTN4 - 1924 - 192
147PROPROVALVALEE5 - 1915 - 191
247PROPROVALVALFF5 - 1915 - 191
148PROPROVALVALEE5 - 1915 - 191
248PROPROVALVALGG5 - 1915 - 191
149PROPROVALVALEE5 - 1915 - 191
249PROPROVALVALIH5 - 1915 - 191
150PROPROVALVALEE5 - 1915 - 191
250PROPROVALVALKI5 - 1915 - 191
151PROPROVALVALEE5 - 1915 - 191
251PROPROVALVALLJ5 - 1915 - 191
152PROPROVALVALEE5 - 1915 - 191
252PROPROVALVALMK5 - 1915 - 191
153PROPROVALVALEE5 - 1915 - 191
253PROPROVALVALNL5 - 1915 - 191
154PROPROPROPROEE5 - 1925 - 192
254PROPROPROPROSM5 - 1925 - 192
155TYRTYRPROPROEE18 - 19218 - 192
255TYRTYRPROPROTN18 - 19218 - 192
156ILEILEVALVALFF4 - 1914 - 191
256ILEILEVALVALGG4 - 1914 - 191
157ILEILEPROPROFF4 - 1924 - 192
257ILEILEPROPROIH4 - 1924 - 192
158ILEILEVALVALFF4 - 1914 - 191
258ILEILEVALVALKI4 - 1914 - 191
159ILEILEVALVALFF4 - 1914 - 191
259ILEILEVALVALLJ4 - 1914 - 191
160ILEILEPROPROFF4 - 1924 - 192
260ILEILEPROPROMK4 - 1924 - 192
161ILEILEPROPROFF4 - 1924 - 192
261ILEILEPROPRONL4 - 1924 - 192
162ILEILEPROPROFF4 - 1924 - 192
262ILEILEPROPROSM4 - 1924 - 192
163ILEILEPROPROFF4 - 1924 - 192
263ILEILEPROPROTN4 - 1924 - 192
164ILEILEGLUGLUGG4 - 1934 - 193
264ILEILEGLUGLUIH4 - 1934 - 193
165ILEILEGLUGLUGG4 - 1934 - 193
265ILEILEGLUGLUKI4 - 1934 - 193
166ILEILEGLUGLUGG4 - 1934 - 193
266ILEILEGLUGLULJ4 - 1934 - 193
167ILEILEVALVALGG4 - 1914 - 191
267ILEILEVALVALMK4 - 1914 - 191
168ILEILEVALVALGG4 - 1914 - 191
268ILEILEVALVALNL4 - 1914 - 191
169ILEILEPROPROGG4 - 1924 - 192
269ILEILEPROPROSM4 - 1924 - 192
170ILEILEPROPROGG4 - 1924 - 192
270ILEILEPROPROTN4 - 1924 - 192
171ILEILEGLUGLUIH4 - 1934 - 193
271ILEILEGLUGLUKI4 - 1934 - 193
172ILEILEGLUGLUIH4 - 1934 - 193
272ILEILEGLUGLULJ4 - 1934 - 193
173ILEILEPROPROIH4 - 1924 - 192
273ILEILEPROPROMK4 - 1924 - 192
174ILEILEPROPROIH4 - 1924 - 192
274ILEILEPROPRONL4 - 1924 - 192
175ILEILEVALVALIH4 - 1914 - 191
275ILEILEVALVALSM4 - 1914 - 191
176ILEILEVALVALIH4 - 1914 - 191
276ILEILEVALVALTN4 - 1914 - 191
177ILEILEGLUGLUKI4 - 1934 - 193
277ILEILEGLUGLULJ4 - 1934 - 193
178ILEILEVALVALKI4 - 1914 - 191
278ILEILEVALVALMK4 - 1914 - 191
179ILEILEVALVALKI4 - 1914 - 191
279ILEILEVALVALNL4 - 1914 - 191
180ILEILEPROPROKI4 - 1924 - 192
280ILEILEPROPROSM4 - 1924 - 192
181ILEILEPROPROKI4 - 1924 - 192
281ILEILEPROPROTN4 - 1924 - 192
182ILEILEVALVALLJ4 - 1914 - 191
282ILEILEVALVALMK4 - 1914 - 191
183ILEILEVALVALLJ4 - 1914 - 191
283ILEILEVALVALNL4 - 1914 - 191
184ILEILEPROPROLJ4 - 1924 - 192
284ILEILEPROPROSM4 - 1924 - 192
185ILEILEPROPROLJ4 - 1924 - 192
285ILEILEPROPROTN4 - 1924 - 192
186ILEILEPROPROMK4 - 1924 - 192
286ILEILEPROPRONL4 - 1924 - 192
187ILEILEPROPROMK4 - 1924 - 192
287ILEILEPROPROSM4 - 1924 - 192
188ILEILEPROPROMK4 - 1924 - 192
288ILEILEPROPROTN4 - 1924 - 192
189ILEILEPROPRONL4 - 1924 - 192
289ILEILEPROPROSM4 - 1924 - 192
190ILEILEPROPRONL4 - 1924 - 192
290ILEILEPROPROTN4 - 1924 - 192
191ILEILEPROPROSM4 - 1924 - 192
291ILEILEPROPROTN4 - 1924 - 192

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 22607.686 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: clpP, SAOUHSC_00790 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G036, endopeptidase Clp
#2: Protein/peptide
9V7-PHE-SER-PRO-YCP-ALA-MP8


Mass: 761.864 Da / Num. of mol.: 14 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O
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: 2.76 Å3/Da / Density % sol: 55.48 % / Description: A 0.3 mM cube formed within 72 hours
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M NaOAc pH 4.5, 18-35% MPD, and 0.02 M CaCl2 / PH range: 4.5-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 6, 2013 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 128084 / % possible obs: 99.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Χ2: 1.863 / Net I/σ(I): 13.1 / Num. measured all: 515914
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.43-2.523.50.212126940.87199.3
2.52-2.623.80.182127420.993199.5
2.62-2.743.90.152127081.151199.5
2.74-2.8840.13127661.357199.7
2.88-3.064.10.108128071.678199.9
3.06-3.34.10.092127801.91100
3.3-3.634.20.075128442.4731100
3.63-4.154.20.061128402.7441100
4.15-5.234.20.056128763.1251100
5.23-504.20.036130271.89199.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
MAR345dtbdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3STA

3sta


Resolution: 2.44→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2013 / WRfactor Rwork: 0.1831 / FOM work R set: 0.8671 / SU B: 14.48 / SU ML: 0.163 / SU R Cruickshank DPI: 0.3374 / SU Rfree: 0.2143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 6556 5.1 %RANDOM
Rwork0.1889 ---
obs0.19 121497 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.16 Å2 / Biso mean: 33.438 Å2 / Biso min: 20.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å21.25 Å2
2---0.91 Å20 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 2.44→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19076 0 756 652 20484
Biso mean--38.45 34.74 -
Num. residues----2508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.01920144
X-RAY DIFFRACTIONr_bond_other_d0.0060.0218920
X-RAY DIFFRACTIONr_angle_refined_deg1.9491.95527276
X-RAY DIFFRACTIONr_angle_other_deg1.168343961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66352480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56125.603846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.645153430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8221593
X-RAY DIFFRACTIONr_chiral_restr0.4750.23169
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0222238
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023699
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A109840.05
12B109840.05
21A110360.06
22C110360.06
31A110340.07
32D110340.07
41A108880.06
42E108880.06
51A110680.06
52F110680.06
61A109900.06
62G109900.06
71A109260.06
72I109260.06
81A110780.06
82K110780.06
91A109920.06
92L109920.06
101A110940.06
102M110940.06
111A110460.06
112N110460.06
121A110600.06
122S110600.06
131A110520.06
132T110520.06
141B110200.05
142C110200.05
151B110920.06
152D110920.06
161B108960.05
162E108960.05
171B110480.04
172F110480.04
181B111140.05
182G111140.05
191B110440.04
192I110440.04
201B111380.04
202K111380.04
211B109680.05
212L109680.05
221B110220.05
222M110220.05
231B110100.04
232N110100.04
241B110040.06
242S110040.06
251B109480.05
252T109480.05
261C110260.07
262D110260.07
271C109200.06
272E109200.06
281C111140.04
282F111140.04
291C109880.06
292G109880.06
301C109820.05
302I109820.05
311C110720.05
312K110720.05
321C110220.05
322L110220.05
331C111240.06
332M111240.06
341C110560.05
342N110560.05
351C110040.06
352S110040.06
361C109980.06
362T109980.06
371D110500.06
372E110500.06
381D110200.06
382F110200.06
391D110860.07
392G110860.07
401D110320.06
402I110320.06
411D111120.07
412K111120.07
421D111200.06
422L111200.06
431D110860.07
432M110860.07
441D110540.06
442N110540.06
451D110060.07
452S110060.07
461D110240.07
462T110240.07
471E109460.06
472F109460.06
481E108840.06
482G108840.06
491E108400.05
492I108400.05
501E109120.07
502K109120.07
511E109200.06
512L109200.06
521E109900.06
522M109900.06
531E109040.06
532N109040.06
541E108720.06
542S108720.06
551E107920.07
552T107920.07
561F110500.05
562G110500.05
571F110000.05
572I110000.05
581F110760.05
582K110760.05
591F110580.04
592L110580.04
601F111340.05
602M111340.05
611F110420.05
612N110420.05
621F110020.06
622S110020.06
631F109900.06
632T109900.06
641G110160.06
642I110160.06
651G111380.05
652K111380.05
661G110560.06
662L110560.06
671G109920.07
672M109920.07
681G109980.06
682N109980.06
691G109960.07
692S109960.07
701G109180.06
702T109180.06
711I110220.04
712K110220.04
721I109420.05
722L109420.05
731I109540.06
732M109540.06
741I109880.04
742N109880.04
751I109300.05
752S109300.05
761I108160.06
762T108160.06
771K110540.06
772L110540.06
781K110140.07
782M110140.07
791K111180.05
792N111180.05
801K110240.06
802S110240.06
811K109780.07
812T109780.07
821L111380.05
822M111380.05
831L109240.05
832N109240.05
841L109880.06
842S109880.06
851L109460.05
852T109460.05
861M110060.06
862N110060.06
871M110380.07
872S110380.07
881M109920.06
882T109920.06
891N109520.06
892S109520.06
901N109600.06
902T109600.06
911S109220.07
912T109220.07
LS refinement shellResolution: 2.435→2.498 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 491 -
Rwork0.221 8644 -
all-9135 -
obs--96.55 %
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)
10.3532-0.04420.09420.46930.08260.57670.0070.04370.0188-0.07320.0048-0.0211-0.01390.0177-0.01190.02040.006-0.01620.07490.02820.099-45.274264.1443-54.2539
20.4738-0.2042-0.28230.5154-0.150.8290.03480.05560.0204-0.072-0.00940.00690.014-0.0009-0.02540.0440.0015-0.03150.07630.01420.0764-33.808546.6449-72.1569
30.82770.1461-0.07890.6498-0.20530.58840.01110.01460.0474-0.05160.0020.0232-0.04930.0299-0.01310.05480.0029-0.01960.0333-0.00370.0122-7.478841.3273-75.9837
40.53550.33740.08420.6837-0.12790.65030.0182-0.02130.01490.0063-0.0217-0.0193-0.03570.02660.00340.01810.00470.00150.02050.00070.002414.012251.5671-62.5879
50.3247-0.0294-0.08030.9543-0.05080.74170.0148-0.01810.04560.0237-0.01130.0119-0.0318-0.0346-0.00350.0066-0.00670.00110.02710.00620.011814.560969.8222-42.4007
60.6125-0.126-0.06850.7482-0.12250.4222-0.01290.03560.050.00170.00540.1012-0.0375-0.04710.00740.03950.0002-0.00010.027-0.00320.0256-6.491482.281-30.3247
70.63350.01940.27530.485-0.14530.4343-0.03520.02130.0168-0.04680.02120.0713-0.058-0.03560.0140.0560.01730.00160.05630.00970.094-33.220379.7815-35.3475
80.40450.09750.30760.4391-0.1060.73180.003-0.0782-0.03520.05930.00430.01970.0275-0.0471-0.00730.05550.00070.03720.11860.03560.0908-38.140743.9854-5.4496
90.6242-0.12340.05620.7118-0.27640.5126-0.014-0.0506-0.05060.04060.0250.02440.0388-0.0108-0.0110.06070.00360.01710.06560.00080.022-11.902447.58481.4608
100.5405-0.2029-0.09090.6061-0.09530.60030.01320.0175-0.0284-0.0084-0.021-0.04310.0490.01170.00770.0269-0.0033-0.00590.04640.00970.009710.602336.3344-9.318
110.29860.09440.01051.04710.01290.72030.0218-0.0056-0.0665-0.0558-0.0489-0.00940.0472-0.00290.02720.02090.0095-0.00780.04230.01830.028712.434918.1361-29.225
120.65460.12580.03330.6621-0.26590.5134-0.006-0.0345-0.0494-0.0041-0.00340.0920.0465-0.05560.00940.06780.002-0.010.012-0.00450.0332-7.60426.7568-43.6874
130.5812-0.0244-0.32750.4102-0.10760.4884-0.0262-0.0213-0.03890.04210.02180.09760.0423-0.0790.00440.0713-0.0293-0.0130.05890.02230.1162-34.679310.6167-41.815
140.29540.0345-0.1790.40130.06330.54220.0196-0.0636-0.00660.05660.00780.01060.0544-0.0541-0.02740.0436-0.01610.01110.11540.04450.1278-48.329127.1371-24.6719
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 192
2X-RAY DIFFRACTION1H1 - 7
3X-RAY DIFFRACTION2B4 - 193
4X-RAY DIFFRACTION2J1 - 7
5X-RAY DIFFRACTION3C4 - 192
6X-RAY DIFFRACTION3O1 - 7
7X-RAY DIFFRACTION4D4 - 193
8X-RAY DIFFRACTION4P1 - 7
9X-RAY DIFFRACTION5E5 - 192
10X-RAY DIFFRACTION5Q1 - 7
11X-RAY DIFFRACTION6F4 - 192
12X-RAY DIFFRACTION6R1 - 7
13X-RAY DIFFRACTION7G4 - 193
14X-RAY DIFFRACTION7U1 - 7
15X-RAY DIFFRACTION8I4 - 193
16X-RAY DIFFRACTION8V1 - 7
17X-RAY DIFFRACTION9K4 - 193
18X-RAY DIFFRACTION9X1 - 7
19X-RAY DIFFRACTION10L4 - 193
20X-RAY DIFFRACTION10Y1 - 7
21X-RAY DIFFRACTION11M4 - 192
22X-RAY DIFFRACTION11Z1 - 7
23X-RAY DIFFRACTION12N4 - 192
24X-RAY DIFFRACTION12a1 - 7
25X-RAY DIFFRACTION13S4 - 192
26X-RAY DIFFRACTION13b1 - 7
27X-RAY DIFFRACTION14T4 - 192
28X-RAY DIFFRACTION14c1 - 7

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