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- PDB-6pmd: Structure of ClpP from Staphylococcus aureus in complex with Acyl... -

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Basic information

Entry
Database: PDB / ID: 6pmd
TitleStructure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide
Components
  • ATP-dependent Clp protease proteolytic subunit
  • SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
KeywordsHYDROLASE/ANTIBIOTIC / ClpP ADEP / ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex
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
SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsGriffith, E.C. / Lee, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI110578 United States
CitationJournal: 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.
History
DepositionJul 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
J: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
O: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
P: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
Q: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
R: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
U: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
V: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
X: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
Y: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
Z: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,86239
Polymers325,20725
Non-polymers1,65414
Water21,0241167
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.377, 125.972, 145.603
Angle α, β, γ (deg.)90.000, 93.770, 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
12ILEILEVALVALAA4 - 1914 - 191
22ILEILEVALVALCC4 - 1914 - 191
13LEULEUVALVALAA3 - 1913 - 191
23LEULEUVALVALDD3 - 1913 - 191
14LEULEUGLUGLUAA3 - 1933 - 193
24LEULEUGLUGLUEE3 - 1933 - 193
15LEULEUVALVALAA3 - 1913 - 191
25LEULEUVALVALFF3 - 1913 - 191
16LEULEUVALVALAA3 - 1913 - 191
26LEULEUVALVALGG3 - 1913 - 191
17LEULEUPROPROAA3 - 1923 - 192
27LEULEUPROPROIH3 - 1923 - 192
18LEULEUVALVALAA3 - 1913 - 191
28LEULEUVALVALKI3 - 1913 - 191
19ILEILEVALVALAA4 - 1914 - 191
29ILEILEVALVALLJ4 - 1914 - 191
110LEULEUGLUGLUAA3 - 1933 - 193
210LEULEUGLUGLUMK3 - 1933 - 193
111LEULEUGLUGLUAA3 - 1933 - 193
211LEULEUGLUGLUNL3 - 1933 - 193
112LEULEUVALVALAA3 - 1913 - 191
212LEULEUVALVALSM3 - 1913 - 191
113LEULEUGLUGLUAA3 - 1933 - 193
213LEULEUGLUGLUTN3 - 1933 - 193
114ILEILEPROPROBB4 - 1924 - 192
214ILEILEPROPROCC4 - 1924 - 192
115ILEILEPROPROBB4 - 1924 - 192
215ILEILEPROPRODD4 - 1924 - 192
116ILEILEPROPROBB4 - 1924 - 192
216ILEILEPROPROEE4 - 1924 - 192
117ILEILEPROPROBB4 - 1924 - 192
217ILEILEPROPROFF4 - 1924 - 192
118ILEILEPROPROBB4 - 1924 - 192
218ILEILEPROPROGG4 - 1924 - 192
119ILEILEVALVALBB4 - 1914 - 191
219ILEILEVALVALIH4 - 1914 - 191
120ILEILEVALVALBB4 - 1914 - 191
220ILEILEVALVALKI4 - 1914 - 191
121ILEILEPROPROBB4 - 1924 - 192
221ILEILEPROPROLJ4 - 1924 - 192
122ILEILEPROPROBB4 - 1924 - 192
222ILEILEPROPROMK4 - 1924 - 192
123ILEILEPROPROBB4 - 1924 - 192
223ILEILEPROPRONL4 - 1924 - 192
124ILEILEPROPROBB4 - 1924 - 192
224ILEILEPROPROSM4 - 1924 - 192
125ILEILEPROPROBB4 - 1924 - 192
225ILEILEPROPROTN4 - 1924 - 192
126ILEILEPROPROCC4 - 1924 - 192
226ILEILEPROPRODD4 - 1924 - 192
127ILEILEPROPROCC4 - 1924 - 192
227ILEILEPROPROEE4 - 1924 - 192
128ILEILEPROPROCC4 - 1924 - 192
228ILEILEPROPROFF4 - 1924 - 192
129ILEILEPROPROCC4 - 1924 - 192
229ILEILEPROPROGG4 - 1924 - 192
130ILEILEVALVALCC4 - 1914 - 191
230ILEILEVALVALIH4 - 1914 - 191
131ILEILEVALVALCC4 - 1914 - 191
231ILEILEVALVALKI4 - 1914 - 191
132ILEILEPROPROCC4 - 1924 - 192
232ILEILEPROPROLJ4 - 1924 - 192
133ILEILEPROPROCC4 - 1924 - 192
233ILEILEPROPROMK4 - 1924 - 192
134ILEILEPROPROCC4 - 1924 - 192
234ILEILEPROPRONL4 - 1924 - 192
135ILEILEPROPROCC4 - 1924 - 192
235ILEILEPROPROSM4 - 1924 - 192
136ILEILEPROPROCC4 - 1924 - 192
236ILEILEPROPROTN4 - 1924 - 192
137LEULEUPROPRODD3 - 1923 - 192
237LEULEUPROPROEE3 - 1923 - 192
138LEULEUPROPRODD3 - 1923 - 192
238LEULEUPROPROFF3 - 1923 - 192
139LEULEUPROPRODD3 - 1923 - 192
239LEULEUPROPROGG3 - 1923 - 192
140LEULEUVALVALDD3 - 1913 - 191
240LEULEUVALVALIH3 - 1913 - 191
141LEULEUPROPRODD3 - 1923 - 192
241LEULEUPROPROKI3 - 1923 - 192
142ILEILEPROPRODD4 - 1924 - 192
242ILEILEPROPROLJ4 - 1924 - 192
143LEULEUPROPRODD3 - 1923 - 192
243LEULEUPROPROMK3 - 1923 - 192
144LEULEUPROPRODD3 - 1923 - 192
244LEULEUPROPRONL3 - 1923 - 192
145LEULEUPROPRODD3 - 1923 - 192
245LEULEUPROPROSM3 - 1923 - 192
146LEULEUPROPRODD3 - 1923 - 192
246LEULEUPROPROTN3 - 1923 - 192
147LEULEUVALVALEE3 - 1913 - 191
247LEULEUVALVALFF3 - 1913 - 191
148LEULEUVALVALEE3 - 1913 - 191
248LEULEUVALVALGG3 - 1913 - 191
149LEULEUGLUGLUEE3 - 1933 - 193
249LEULEUGLUGLUIH3 - 1933 - 193
150LEULEUPROPROEE3 - 1923 - 192
250LEULEUPROPROKI3 - 1923 - 192
151ILEILEPROPROEE4 - 1924 - 192
251ILEILEPROPROLJ4 - 1924 - 192
152LEULEUGLUGLUEE3 - 1933 - 193
252LEULEUGLUGLUMK3 - 1933 - 193
153LEULEUGLUGLUEE3 - 1933 - 193
253LEULEUGLUGLUNL3 - 1933 - 193
154LEULEUPROPROEE3 - 1923 - 192
254LEULEUPROPROSM3 - 1923 - 192
155LEULEUGLUGLUEE3 - 1933 - 193
255LEULEUGLUGLUTN3 - 1933 - 193
156LEULEUPROPROFF3 - 1923 - 192
256LEULEUPROPROGG3 - 1923 - 192
157LEULEUPROPROFF3 - 1923 - 192
257LEULEUPROPROIH3 - 1923 - 192
158LEULEUPROPROFF3 - 1923 - 192
258LEULEUPROPROKI3 - 1923 - 192
159ILEILEPROPROFF4 - 1924 - 192
259ILEILEPROPROLJ4 - 1924 - 192
160LEULEUPROPROFF3 - 1923 - 192
260LEULEUPROPROMK3 - 1923 - 192
161LEULEUVALVALFF3 - 1913 - 191
261LEULEUVALVALNL3 - 1913 - 191
162LEULEUPROPROFF3 - 1923 - 192
262LEULEUPROPROSM3 - 1923 - 192
163LEULEUPROPROFF3 - 1923 - 192
263LEULEUPROPROTN3 - 1923 - 192
164LEULEUPROPROGG3 - 1923 - 192
264LEULEUPROPROIH3 - 1923 - 192
165LEULEUPROPROGG3 - 1923 - 192
265LEULEUPROPROKI3 - 1923 - 192
166ILEILEPROPROGG4 - 1924 - 192
266ILEILEPROPROLJ4 - 1924 - 192
167LEULEUPROPROGG3 - 1923 - 192
267LEULEUPROPROMK3 - 1923 - 192
168LEULEUVALVALGG3 - 1913 - 191
268LEULEUVALVALNL3 - 1913 - 191
169LEULEUPROPROGG3 - 1923 - 192
269LEULEUPROPROSM3 - 1923 - 192
170LEULEUPROPROGG3 - 1923 - 192
270LEULEUPROPROTN3 - 1923 - 192
171LEULEUPROPROIH3 - 1923 - 192
271LEULEUPROPROKI3 - 1923 - 192
172ILEILEVALVALIH4 - 1914 - 191
272ILEILEVALVALLJ4 - 1914 - 191
173LEULEUGLUGLUIH3 - 1933 - 193
273LEULEUGLUGLUMK3 - 1933 - 193
174LEULEUGLUGLUIH3 - 1933 - 193
274LEULEUGLUGLUNL3 - 1933 - 193
175LEULEUVALVALIH3 - 1913 - 191
275LEULEUVALVALSM3 - 1913 - 191
176LEULEUGLUGLUIH3 - 1933 - 193
276LEULEUGLUGLUTN3 - 1933 - 193
177ILEILEVALVALKI4 - 1914 - 191
277ILEILEVALVALLJ4 - 1914 - 191
178LEULEUPROPROKI3 - 1923 - 192
278LEULEUPROPROMK3 - 1923 - 192
179LEULEUPROPROKI3 - 1923 - 192
279LEULEUPROPRONL3 - 1923 - 192
180LEULEUPROPROKI3 - 1923 - 192
280LEULEUPROPROSM3 - 1923 - 192
181LEULEUPROPROKI3 - 1923 - 192
281LEULEUPROPROTN3 - 1923 - 192
182ILEILEPROPROLJ4 - 1924 - 192
282ILEILEPROPROMK4 - 1924 - 192
183ILEILEPROPROLJ4 - 1924 - 192
283ILEILEPROPRONL4 - 1924 - 192
184ILEILEPROPROLJ4 - 1924 - 192
284ILEILEPROPROSM4 - 1924 - 192
185ILEILEPROPROLJ4 - 1924 - 192
285ILEILEPROPROTN4 - 1924 - 192
186LEULEUGLUGLUMK3 - 1933 - 193
286LEULEUGLUGLUNL3 - 1933 - 193
187LEULEUPROPROMK3 - 1923 - 192
287LEULEUPROPROSM3 - 1923 - 192
188LEULEUGLUGLUMK3 - 1933 - 193
288LEULEUGLUGLUTN3 - 1933 - 193
189LEULEUPROPRONL3 - 1923 - 192
289LEULEUPROPROSM3 - 1923 - 192
190LEULEUGLUGLUNL3 - 1933 - 193
290LEULEUGLUGLUTN3 - 1933 - 193
191LEULEUPROPROSM3 - 1923 - 192
291LEULEUPROPROTN3 - 1923 - 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G036, endopeptidase Clp
#2: Protein/peptide
SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide


Type: Oligopeptide / Class: Antibiotic / Mass: 790.894 Da / Num. of mol.: 11 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M NaOAc pH 4.5, 18-35% MPD, 0.02M CaCl2 / PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 166305 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.065 / Rrim(I) all: 0.15 / Χ2: 1.142 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.22-2.2640.55278720.7490.3090.6361.07795.1
2.26-2.34.60.51983130.8250.2670.5851.089100
2.3-2.3450.48583300.8350.2370.5411.087100
2.34-2.395.20.45182660.880.2160.5011.077100
2.39-2.445.20.41282860.8960.1970.4581.079100
2.44-2.55.20.3783270.9080.1770.4111.1100
2.5-2.565.20.32283360.9260.1550.3581.156100
2.56-2.635.30.2983030.9330.1390.3231.167100
2.63-2.715.30.2683280.9420.1250.2891.193100
2.71-2.85.30.22483120.9570.1070.2491.223100
2.8-2.95.30.20483070.960.0980.2261.212100
2.9-3.015.30.17283290.9690.0830.1921.21100
3.01-3.155.30.15483680.9740.0740.1721.195100
3.15-3.325.30.13783160.9770.0660.1521.239100
3.32-3.525.30.12183110.9810.0580.1341.243100
3.52-3.85.40.10683570.9840.0510.1181.249100
3.8-4.185.40.09783620.9860.0470.1081.225100
4.18-4.785.40.09583650.9870.0460.1061.256100
4.78-6.025.40.08584170.9910.040.0940.977100
6.02-505.30.06385000.9960.030.070.74299.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3STA

3sta


Resolution: 2.21→38.8 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.341 / SU ML: 0.134 / SU R Cruickshank DPI: 0.2445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.189
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 8358 5 %RANDOM
Rwork0.1995 ---
obs0.2009 157921 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.49 Å2 / Biso mean: 32.511 Å2 / Biso min: 11.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20.32 Å2
2---0.45 Å20 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 2.21→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19415 0 717 1167 21299
Biso mean--37.26 37.18 -
Num. residues----2548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01420420
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719014
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.69827633
X-RAY DIFFRACTIONr_angle_other_deg0.9571.69144467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08252522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84523.807951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.502153522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1091599
X-RAY DIFFRACTIONr_chiral_restr0.2660.22894
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023382
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A55710.04
12B55710.04
21A56130.04
22C56130.04
31A56450.04
32D56450.04
41A56450.04
42E56450.04
51A55950.05
52F55950.05
61A56030.05
62G56030.05
71A56380.04
72I56380.04
81A56410.05
82K56410.05
91A55930.05
92L55930.05
101A56100.04
102M56100.04
111A56590.04
112N56590.04
121A56500.04
122S56500.04
131A56430.04
132T56430.04
141B56650.05
142C56650.05
151B56140.05
152D56140.05
161B56140.04
162E56140.04
171B55910.04
172F55910.04
181B56390.05
182G56390.05
191B56550.03
192I56550.03
201B56490.06
202K56490.06
211B56510.06
212L56510.06
221B56060.04
222M56060.04
231B56130.05
232N56130.05
241B56450.05
242S56450.05
251B55970.05
252T55970.05
261C56790.04
262D56790.04
271C56180.05
272E56180.05
281C55920.06
282F55920.06
291C56510.05
292G56510.05
301C56370.05
302I56370.05
311C56920.06
312K56920.06
321C56940.05
322L56940.05
331C56000.05
332M56000.05
341C56480.05
342N56480.05
351C56680.05
352S56680.05
361C56360.05
362T56360.05
371D56380.05
372E56380.05
381D56030.05
382F56030.05
391D56400.05
392G56400.05
401D56350.04
402I56350.04
411D57010.05
412K57010.05
421D56720.04
422L56720.04
431D55970.05
432M55970.05
441D56500.05
442N56500.05
451D56890.05
452S56890.05
461D56420.04
462T56420.04
471E55980.05
472F55980.05
481E55980.06
482G55980.06
491E56560.05
492I56560.05
501E56320.06
502K56320.06
511E55930.05
512L55930.05
521E56150.04
522M56150.04
531E56740.04
532N56740.04
541E56690.05
542S56690.05
551E56410.04
552T56410.04
561F56090.06
562G56090.06
571F56450.05
572I56450.05
581F56290.07
582K56290.07
591F55700.07
592L55700.07
601F56010.05
602M56010.05
611F56040.06
612N56040.06
621F56210.06
622S56210.06
631F56000.06
632T56000.06
641G56760.05
642I56760.05
651G56920.06
652K56920.06
661G56260.05
662L56260.05
671G56130.05
672M56130.05
681G56310.06
682N56310.06
691G56490.05
692S56490.05
701G56210.05
702T56210.05
711I56770.06
712K56770.06
721I56200.05
722L56200.05
731I56340.04
732M56340.04
741I56860.05
742N56860.05
751I56490.05
752S56490.05
761I56380.05
762T56380.05
771K56370.07
772L56370.07
781K56180.06
782M56180.06
791K56570.06
792N56570.06
801K57010.05
802S57010.05
811K56380.06
812T56380.06
821L55630.05
822M55630.05
831L56530.06
832N56530.06
841L56350.06
842S56350.06
851L56320.05
852T56320.05
861M56040.05
862N56040.05
871M56130.05
872S56130.05
881M56050.05
882T56050.05
891N56620.05
892S56620.05
901N56820.05
902T56820.05
911S56410.05
912T56410.05
LS refinement shellResolution: 2.211→2.269 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 450 -
Rwork0.248 8819 -
all-9269 -
obs--74.54 %

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