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- PDB-5dzk: Crystal structure of the active form of the proteolytic complex c... -

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Basic information

Entry
Database: PDB / ID: 5dzk
TitleCrystal structure of the active form of the proteolytic complex clpP1 and clpP2
Components
  • ATP-dependent Clp protease proteolytic subunit 1
  • ATP-dependent Clp protease proteolytic subunit 2
  • BEZ-LEU-LEU
KeywordsHYDROLASE
Function / homology
Function and homology information


endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / peptidoglycan-based cell wall / ATPase binding / serine-type endopeptidase activity / proteolysis / plasma membrane / cytosol / 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
Inhibitor BEZ-LEU-LEU / ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 1 / ATP-dependent Clp protease proteolytic subunit 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.07 Å
AuthorsLI, M. / Wlodawer, A. / Maurizi, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure and Functional Properties of the Active Form of the Proteolytic Complex, ClpP1P2, from Mycobacterium tuberculosis.
Authors: Li, M. / Kandror, O. / Akopian, T. / Dharkar, P. / Wlodawer, A. / Maurizi, M.R. / Goldberg, A.L.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references

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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 2
O: BEZ-LEU-LEU
B: ATP-dependent Clp protease proteolytic subunit 2
P: BEZ-LEU-LEU
C: ATP-dependent Clp protease proteolytic subunit 2
Q: BEZ-LEU-LEU
D: ATP-dependent Clp protease proteolytic subunit 2
R: BEZ-LEU-LEU
E: ATP-dependent Clp protease proteolytic subunit 2
S: BEZ-LEU-LEU
F: ATP-dependent Clp protease proteolytic subunit 2
T: BEZ-LEU-LEU
G: ATP-dependent Clp protease proteolytic subunit 2
U: BEZ-LEU-LEU
H: ATP-dependent Clp protease proteolytic subunit 1
V: BEZ-LEU-LEU
I: ATP-dependent Clp protease proteolytic subunit 1
W: BEZ-LEU-LEU
J: ATP-dependent Clp protease proteolytic subunit 1
X: BEZ-LEU-LEU
K: ATP-dependent Clp protease proteolytic subunit 1
Y: BEZ-LEU-LEU
L: ATP-dependent Clp protease proteolytic subunit 1
Z: BEZ-LEU-LEU
M: ATP-dependent Clp protease proteolytic subunit 1
1: BEZ-LEU-LEU
N: ATP-dependent Clp protease proteolytic subunit 1
2: BEZ-LEU-LEU
a: ATP-dependent Clp protease proteolytic subunit 2
o: BEZ-LEU-LEU
b: ATP-dependent Clp protease proteolytic subunit 2
p: BEZ-LEU-LEU
c: ATP-dependent Clp protease proteolytic subunit 2
q: BEZ-LEU-LEU
d: ATP-dependent Clp protease proteolytic subunit 2
r: BEZ-LEU-LEU
e: ATP-dependent Clp protease proteolytic subunit 2
s: BEZ-LEU-LEU
f: ATP-dependent Clp protease proteolytic subunit 2
t: BEZ-LEU-LEU
g: ATP-dependent Clp protease proteolytic subunit 2
u: BEZ-LEU-LEU
h: ATP-dependent Clp protease proteolytic subunit 1
v: BEZ-LEU-LEU
i: ATP-dependent Clp protease proteolytic subunit 1
w: BEZ-LEU-LEU
j: ATP-dependent Clp protease proteolytic subunit 1
x: BEZ-LEU-LEU
k: ATP-dependent Clp protease proteolytic subunit 1
y: BEZ-LEU-LEU
l: ATP-dependent Clp protease proteolytic subunit 1
z: BEZ-LEU-LEU
m: ATP-dependent Clp protease proteolytic subunit 1
3: BEZ-LEU-LEU
n: ATP-dependent Clp protease proteolytic subunit 1
4: BEZ-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)643,82256
Polymers643,82256
Non-polymers00
Water95553
1
A: ATP-dependent Clp protease proteolytic subunit 2
O: BEZ-LEU-LEU
B: ATP-dependent Clp protease proteolytic subunit 2
P: BEZ-LEU-LEU
C: ATP-dependent Clp protease proteolytic subunit 2
Q: BEZ-LEU-LEU
D: ATP-dependent Clp protease proteolytic subunit 2
R: BEZ-LEU-LEU
E: ATP-dependent Clp protease proteolytic subunit 2
S: BEZ-LEU-LEU
F: ATP-dependent Clp protease proteolytic subunit 2
T: BEZ-LEU-LEU
G: ATP-dependent Clp protease proteolytic subunit 2
U: BEZ-LEU-LEU
H: ATP-dependent Clp protease proteolytic subunit 1
V: BEZ-LEU-LEU
I: ATP-dependent Clp protease proteolytic subunit 1
W: BEZ-LEU-LEU
J: ATP-dependent Clp protease proteolytic subunit 1
X: BEZ-LEU-LEU
K: ATP-dependent Clp protease proteolytic subunit 1
Y: BEZ-LEU-LEU
L: ATP-dependent Clp protease proteolytic subunit 1
Z: BEZ-LEU-LEU
M: ATP-dependent Clp protease proteolytic subunit 1
1: BEZ-LEU-LEU
N: ATP-dependent Clp protease proteolytic subunit 1
2: BEZ-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)321,91128
Polymers321,91128
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
a: ATP-dependent Clp protease proteolytic subunit 2
o: BEZ-LEU-LEU
b: ATP-dependent Clp protease proteolytic subunit 2
p: BEZ-LEU-LEU
c: ATP-dependent Clp protease proteolytic subunit 2
q: BEZ-LEU-LEU
d: ATP-dependent Clp protease proteolytic subunit 2
r: BEZ-LEU-LEU
e: ATP-dependent Clp protease proteolytic subunit 2
s: BEZ-LEU-LEU
f: ATP-dependent Clp protease proteolytic subunit 2
t: BEZ-LEU-LEU
g: ATP-dependent Clp protease proteolytic subunit 2
u: BEZ-LEU-LEU
h: ATP-dependent Clp protease proteolytic subunit 1
v: BEZ-LEU-LEU
i: ATP-dependent Clp protease proteolytic subunit 1
w: BEZ-LEU-LEU
j: ATP-dependent Clp protease proteolytic subunit 1
x: BEZ-LEU-LEU
k: ATP-dependent Clp protease proteolytic subunit 1
y: BEZ-LEU-LEU
l: ATP-dependent Clp protease proteolytic subunit 1
z: BEZ-LEU-LEU
m: ATP-dependent Clp protease proteolytic subunit 1
3: BEZ-LEU-LEU
n: ATP-dependent Clp protease proteolytic subunit 1
4: BEZ-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)321,91128
Polymers321,91128
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)205.940, 183.350, 188.450
Angle α, β, γ (deg.)90.00, 94.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27a
18A
28b
19A
29c
110A
210d
111A
211e
112A
212f
113A
213g
114B
214C
115B
215D
116B
216E
117B
217F
118B
218G
119B
219a
120B
220b
121B
221c
122B
222d
123B
223e
124B
224f
125B
225g
126C
226D
127C
227E
128C
228F
129C
229G
130C
230a
131C
231b
132C
232c
133C
233d
134C
234e
135C
235f
136C
236g
137D
237E
138D
238F
139D
239G
140D
240a
141D
241b
142D
242c
143D
243d
144D
244e
145D
245f
146D
246g
147E
247F
148E
248G
149E
249a
150E
250b
151E
251c
152E
252d
153E
253e
154E
254f
155E
255g
156F
256G
157F
257a
158F
258b
159F
259c
160F
260d
161F
261e
162F
262f
163F
263g
164G
264a
165G
265b
166G
266c
167G
267d
168G
268e
169G
269f
170G
270g
171H
271I
172H
272J
173H
273K
174H
274L
175H
275M
176H
276N
177H
277h
178H
278i
179H
279j
180H
280k
181H
281l
182H
282m
183H
283n
184I
284J
185I
285K
186I
286L
187I
287M
188I
288N
189I
289h
190I
290i
191I
291j
192I
292k
193I
293l
194I
294m
195I
295n
196J
296K
197J
297L
198J
298M
199J
299N
1100J
2100h
1101J
2101i
1102J
2102j
1103J
2103k
1104J
2104l
1105J
2105m
1106J
2106n
1107K
2107L
1108K
2108M
1109K
2109N
1110K
2110h
1111K
2111i
1112K
2112j
1113K
2113k
1114K
2114l
1115K
2115m
1116K
2116n
1117L
2117M
1118L
2118N
1119L
2119h
1120L
2120i
1121L
2121j
1122L
2122k
1123L
2123l
1124L
2124m
1125L
2125n
1126M
2126N
1127M
2127h
1128M
2128i
1129M
2129j
1130M
2130k
1131M
2131l
1132M
2132m
1133M
2133n
1134N
2134h
1135N
2135i
1136N
2136j
1137N
2137k
1138N
2138l
1139N
2139m
1140N
2140n
1141a
2141b
1142a
2142c
1143a
2143d
1144a
2144e
1145a
2145f
1146a
2146g
1147b
2147c
1148b
2148d
1149b
2149e
1150b
2150f
1151b
2151g
1152c
2152d
1153c
2153e
1154c
2154f
1155c
2155g
1156d
2156e
1157d
2157f
1158d
2158g
1159e
2159f
1160e
2160g
1161f
2161g
1162h
2162i
1163h
2163j
1164h
2164k
1165h
2165l
1166h
2166m
1167h
2167n
1168i
2168j
1169i
2169k
1170i
2170l
1171i
2171m
1172i
2172n
1173j
2173k
1174j
2174l
1175j
2175m
1176j
2176n
1177k
2177l
1178k
2178m
1179k
2179n
1180l
2180m
1181l
2181n
1182m
2182n

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 209
2010B15 - 209
1020A15 - 210
2020C15 - 210
1030A15 - 210
2030D15 - 210
1040A15 - 209
2040E15 - 209
1050A15 - 210
2050F15 - 210
1060A15 - 208
2060G15 - 208
1070A15 - 209
2070a15 - 209
1080A15 - 209
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1090A15 - 209
2090c15 - 209
10100A15 - 210
20100d15 - 210
10110A15 - 209
20110e15 - 209
10120A15 - 210
20120f15 - 210
10130A15 - 210
20130g15 - 210
10140B15 - 209
20140C15 - 209
10150B15 - 209
20150D15 - 209
10160B15 - 214
20160E15 - 214
10170B15 - 209
20170F15 - 209
10180B15 - 208
20180G15 - 208
10190B15 - 210
20190a15 - 210
10200B15 - 214
20200b15 - 214
10210B15 - 210
20210c15 - 210
10220B15 - 209
20220d15 - 209
10230B15 - 214
20230e15 - 214
10240B15 - 209
20240f15 - 209
10250B15 - 209
20250g15 - 209
10260C15 - 210
20260D15 - 210
10270C15 - 209
20270E15 - 209
10280C15 - 210
20280F15 - 210
10290C15 - 208
20290G15 - 208
10300C15 - 209
20300a15 - 209
10310C15 - 209
20310b15 - 209
10320C15 - 209
20320c15 - 209
10330C15 - 210
20330d15 - 210
10340C15 - 209
20340e15 - 209
10350C15 - 210
20350f15 - 210
10360C15 - 210
20360g15 - 210
10370D15 - 209
20370E15 - 209
10380D15 - 210
20380F15 - 210
10390D15 - 208
20390G15 - 208
10400D15 - 209
20400a15 - 209
10410D15 - 209
20410b15 - 209
10420D15 - 209
20420c15 - 209
10430D15 - 210
20430d15 - 210
10440D15 - 209
20440e15 - 209
10450D15 - 210
20450f15 - 210
10460D15 - 210
20460g15 - 210
10470E15 - 209
20470F15 - 209
10480E15 - 208
20480G15 - 208
10490E15 - 210
20490a15 - 210
10500E15 - 214
20500b15 - 214
10510E15 - 210
20510c15 - 210
10520E15 - 209
20520d15 - 209
10530E15 - 214
20530e15 - 214
10540E15 - 209
20540f15 - 209
10550E15 - 209
20550g15 - 209
10560F15 - 208
20560G15 - 208
10570F15 - 209
20570a15 - 209
10580F15 - 209
20580b15 - 209
10590F15 - 209
20590c15 - 209
10600F15 - 210
20600d15 - 210
10610F15 - 209
20610e15 - 209
10620F15 - 210
20620f15 - 210
10630F15 - 210
20630g15 - 210
10640G15 - 208
20640a15 - 208
10650G15 - 208
20650b15 - 208
10660G15 - 208
20660c15 - 208
10670G15 - 208
20670d15 - 208
10680G15 - 208
20680e15 - 208
10690G15 - 208
20690f15 - 208
10700G15 - 208
20700g15 - 208
10710H15 - 192
20710I15 - 192
10720H15 - 192
20720J15 - 192
10730H15 - 192
20730K15 - 192
10740H15 - 192
20740L15 - 192
10750H15 - 192
20750M15 - 192
10760H15 - 191
20760N15 - 191
10770H15 - 192
20770h15 - 192
10780H15 - 192
20780i15 - 192
10790H15 - 192
20790j15 - 192
10800H15 - 192
20800k15 - 192
10810H15 - 192
20810l15 - 192
10820H15 - 192
20820m15 - 192
10830H15 - 192
20830n15 - 192
10840I15 - 192
20840J15 - 192
10850I15 - 192
20850K15 - 192
10860I15 - 192
20860L15 - 192
10870I15 - 192
20870M15 - 192
10880I15 - 191
20880N15 - 191
10890I15 - 192
20890h15 - 192
10900I15 - 192
20900i15 - 192
10910I15 - 192
20910j15 - 192
10920I15 - 192
20920k15 - 192
10930I15 - 192
20930l15 - 192
10940I15 - 192
20940m15 - 192
10950I15 - 192
20950n15 - 192
10960J15 - 192
20960K15 - 192
10970J15 - 192
20970L15 - 192
10980J15 - 192
20980M15 - 192
10990J15 - 191
20990N15 - 191
101000J15 - 192
201000h15 - 192
101010J15 - 192
201010i15 - 192
101020J15 - 192
201020j15 - 192
101030J15 - 192
201030k15 - 192
101040J15 - 192
201040l15 - 192
101050J15 - 192
201050m15 - 192
101060J15 - 192
201060n15 - 192
101070K15 - 192
201070L15 - 192
101080K15 - 192
201080M15 - 192
101090K15 - 191
201090N15 - 191
101100K15 - 192
201100h15 - 192
101110K15 - 192
201110i15 - 192
101120K15 - 192
201120j15 - 192
101130K15 - 192
201130k15 - 192
101140K15 - 192
201140l15 - 192
101150K15 - 192
201150m15 - 192
101160K15 - 192
201160n15 - 192
101170L15 - 192
201170M15 - 192
101180L15 - 191
201180N15 - 191
101190L15 - 192
201190h15 - 192
101200L15 - 192
201200i15 - 192
101210L15 - 192
201210j15 - 192
101220L15 - 192
201220k15 - 192
101230L15 - 192
201230l15 - 192
101240L15 - 192
201240m15 - 192
101250L15 - 192
201250n15 - 192
101260M15 - 191
201260N15 - 191
101270M15 - 192
201270h15 - 192
101280M15 - 192
201280i15 - 192
101290M15 - 192
201290j15 - 192
101300M15 - 192
201300k15 - 192
101310M15 - 192
201310l15 - 192
101320M15 - 192
201320m15 - 192
101330M15 - 192
201330n15 - 192
101340N15 - 191
201340h15 - 191
101350N15 - 191
201350i15 - 191
101360N15 - 191
201360j15 - 191
101370N15 - 191
201370k15 - 191
101380N15 - 191
201380l15 - 191
101390N15 - 191
201390m15 - 191
101400N15 - 191
201400n15 - 191
101410a15 - 210
201410b15 - 210
101420a15 - 211
201420c15 - 211
101430a15 - 209
201430d15 - 209
101440a15 - 210
201440e15 - 210
101450a15 - 209
201450f15 - 209
101460a15 - 209
201460g15 - 209
101470b15 - 210
201470c15 - 210
101480b15 - 209
201480d15 - 209
101490b15 - 214
201490e15 - 214
101500b15 - 209
201500f15 - 209
101510b15 - 209
201510g15 - 209
101520c15 - 209
201520d15 - 209
101530c15 - 210
201530e15 - 210
101540c15 - 209
201540f15 - 209
101550c15 - 209
201550g15 - 209
101560d15 - 209
201560e15 - 209
101570d15 - 210
201570f15 - 210
101580d15 - 210
201580g15 - 210
101590e15 - 209
201590f15 - 209
101600e15 - 209
201600g15 - 209
101610f15 - 210
201610g15 - 210
101620h15 - 192
201620i15 - 192
101630h15 - 192
201630j15 - 192
101640h15 - 192
201640k15 - 192
101650h15 - 192
201650l15 - 192
101660h15 - 192
201660m15 - 192
101670h15 - 192
201670n15 - 192
101680i15 - 192
201680j15 - 192
101690i15 - 192
201690k15 - 192
101700i15 - 192
201700l15 - 192
101710i15 - 192
201710m15 - 192
101720i15 - 192
201720n15 - 192
101730j15 - 192
201730k15 - 192
101740j15 - 192
201740l15 - 192
101750j15 - 192
201750m15 - 192
101760j15 - 192
201760n15 - 192
101770k15 - 192
201770l15 - 192
101780k15 - 192
201780m15 - 192
101790k15 - 192
201790n15 - 192
101800l15 - 192
201800m15 - 192
101810l15 - 192
201810n15 - 192
101820m15 - 192
201820n15 - 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
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43
44
45
46
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63
64
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72
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81
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83
84
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90
91
92
93
94
95
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98
99
100
101
102
103
104
105
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107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182

-
Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 23562.754 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: clpP2, MT2535 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPC2, UniProt: P9WPC3*PLUS, endopeptidase Clp
#2: Protein/peptide ...
BEZ-LEU-LEU


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 348.437 Da / Num. of mol.: 28 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Inhibitor BEZ-LEU-LEU
#3: Protein
ATP-dependent Clp protease proteolytic subunit 1 / Endopeptidase Clp 1


Mass: 21727.664 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: clpP1, clpP, MT2536 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPC4, UniProt: P9WPC5*PLUS, endopeptidase Clp
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.07→100 Å / Num. obs: 129368 / % possible obs: 99.5 % / Redundancy: 4.22 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.33
Reflection shellResolution: 3.07→3.15 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.29

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 3.07→72.24 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 44.69 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23167 6092 5 %RANDOM
Rwork0.19822 ---
obs0.19989 115022 93.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.125 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å2-0 Å2-1.35 Å2
2---2.54 Å2-0 Å2
3---6.1 Å2
Refinement stepCycle: LAST / Resolution: 3.07→72.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40923 0 0 53 40976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01941525
X-RAY DIFFRACTIONr_bond_other_d0.0090.0240413
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.98356129
X-RAY DIFFRACTIONr_angle_other_deg2.056392779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27755254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01224.1861782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.749157249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.33215294
X-RAY DIFFRACTIONr_chiral_restr0.0910.26518
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0246938
X-RAY DIFFRACTIONr_gen_planes_other0.0070.029056
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A116420.07
12B116420.07
21A114790.08
22C114790.08
31A115240.09
32D115240.09
41A116190.07
42E116190.07
51A114540.09
52F114540.09
61A115380.07
62G115380.07
71A116530.07
72a116530.07
81A115630.07
82b115630.07
91A114630.09
92c114630.09
101A115080.08
102d115080.08
111A114520.09
112e114520.09
121A116630.07
122f116630.07
131A116240.07
132g116240.07
141B114320.09
142C114320.09
151B115110.09
152D115110.09
161B116810.08
162E116810.08
171B114250.08
172F114250.08
181B115100.07
182G115100.07
191B115740.07
192a115740.07
201B115480.09
202b115480.09
211B115990.07
212c115990.07
221B115450.08
222d115450.08
231B116270.08
232e116270.08
241B115480.08
242f115480.08
251B116090.07
252g116090.07
261C115090.09
262D115090.09
271C115900.08
272E115900.08
281C113970.09
282F113970.09
291C115010.08
292G115010.08
301C114660.08
302a114660.08
311C114080.08
312b114080.08
321C114780.08
322c114780.08
331C114830.08
332d114830.08
341C113680.09
342e113680.09
351C116020.08
352f116020.08
361C115570.08
362g115570.08
371D116490.08
372E116490.08
381D114980.1
382F114980.1
391D114850.08
392G114850.08
401D115060.08
402a115060.08
411D114520.09
412b114520.09
421D114970.09
422c114970.09
431D116520.09
432d116520.09
441D115780.09
442e115780.09
451D116170.09
452f116170.09
461D115920.09
462g115920.09
471E114230.09
472F114230.09
481E116980.06
482G116980.06
491E118220.05
492a118220.05
501E116690.08
502b116690.08
511E117080.07
512c117080.07
521E115760.08
522d115760.08
531E118250.07
532e118250.07
541E117400.07
542f117400.07
551E117420.07
552g117420.07
561F113640.09
562G113640.09
571F113640.09
572a113640.09
581F113620.09
582b113620.09
591F114620.09
592c114620.09
601F115680.08
602d115680.08
611F114990.09
612e114990.09
621F115640.08
622f115640.08
631F114870.09
632g114870.09
641G115850.06
642a115850.06
651G114820.08
652b114820.08
661G115450.08
662c115450.08
671G114290.08
672d114290.08
681G115150.08
682e115150.08
691G116540.07
692f116540.07
701G116120.07
702g116120.07
711H104080.08
712I104080.08
721H105050.07
722J105050.07
731H103430.09
732K103430.09
741H103350.09
742L103350.09
751H103330.09
752M103330.09
761H102500.09
762N102500.09
771H104340.08
772h104340.08
781H104580.09
782i104580.09
791H103700.08
792j103700.08
801H103790.09
802k103790.09
811H104720.08
812l104720.08
821H104570.09
822m104570.09
831H103190.09
832n103190.09
841I104160.08
842J104160.08
851I102240.09
852K102240.09
861I102590.1
862L102590.1
871I103940.09
872M103940.09
881I102590.08
882N102590.08
891I102630.09
892h102630.09
901I104280.09
902i104280.09
911I104490.08
912j104490.08
921I102420.1
922k102420.1
931I104340.08
932l104340.08
941I103370.09
942m103370.09
951I103140.09
952n103140.09
961J102800.08
962K102800.08
971J103880.08
972L103880.08
981J103860.09
982M103860.09
991J102370.08
992N102370.08
1001J104080.07
1002h104080.07
1011J105190.07
1012i105190.07
1021J103950.08
1022j103950.08
1031J103480.08
1032k103480.08
1041J105210.07
1042l105210.07
1051J104630.07
1052m104630.07
1061J103540.07
1062n103540.07
1071K104030.09
1072L104030.09
1081K101640.1
1082M101640.1
1091K101700.09
1092N101700.09
1101K104790.08
1102h104790.08
1111K102690.09
1112i102690.09
1121K101870.09
1122j101870.09
1131K104030.09
1132k104030.09
1141K103260.08
1142l103260.08
1151K102850.09
1152m102850.09
1161K103700.08
1162n103700.08
1171L102930.09
1172M102930.09
1181L101690.09
1182N101690.09
1191L104230.09
1192h104230.09
1201L104050.08
1202i104050.08
1211L102410.09
1212j102410.09
1221L104630.07
1222k104630.07
1231L103490.09
1232l103490.09
1241L103230.09
1242m103230.09
1251L104670.08
1252n104670.08
1261M102510.09
1262N102510.09
1271M102570.09
1272h102570.09
1281M103770.09
1282i103770.09
1291M103020.09
1292j103020.09
1301M101880.11
1302k101880.11
1311M104320.08
1312l104320.08
1321M104350.08
1322m104350.08
1331M103560.09
1332n103560.09
1341N102080.09
1342h102080.09
1351N102320.09
1352i102320.09
1361N102780.08
1362j102780.08
1371N102530.09
1372k102530.09
1381N102180.09
1382l102180.09
1391N103400.08
1392m103400.08
1401N101770.09
1402n101770.09
1411a115930.07
1412b115930.07
1421a115720.08
1422c115720.08
1431a114860.08
1432d114860.08
1441a115630.07
1442e115630.07
1451a116850.06
1452f116850.06
1461a116360.07
1462g116360.07
1471b114570.09
1472c114570.09
1481b115350.08
1482d115350.08
1491b116330.09
1492e116330.09
1501b115720.08
1502f115720.08
1511b116250.08
1512g116250.08
1521c114700.08
1522d114700.08
1531c116430.07
1532e116430.07
1541c115720.09
1542f115720.09
1551c116310.07
1552g116310.07
1561d115880.08
1562e115880.08
1571d115560.08
1572f115560.08
1581d115660.08
1582g115660.08
1591e115270.08
1592f115270.08
1601e116520.06
1602g116520.06
1611f117340.07
1612g117340.07
1621h103660.09
1622i103660.09
1631h102220.09
1632j102220.09
1641h105160.08
1642k105160.08
1651h103850.08
1652l103850.08
1661h103760.08
1662m103760.08
1671h103860.08
1672n103860.08
1681i103210.09
1682j103210.09
1691i102350.1
1692k102350.1
1701i104060.08
1702l104060.08
1711i104380.08
1712m104380.08
1721i103770.08
1722n103770.08
1731j102520.09
1732k102520.09
1741j104420.07
1742l104420.07
1751j103000.08
1752m103000.08
1761j103350.08
1762n103350.08
1771k103720.08
1772l103720.08
1781k102750.1
1782m102750.1
1791k103750.09
1792n103750.09
1801l103800.08
1802m103800.08
1811l103900.09
1812n103900.09
1821m102690.09
1822n102690.09
LS refinement shellResolution: 3.07→3.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 384 -
Rwork0.313 7464 -
obs--81.96 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.55960.2561-0.46741.3128-0.23990.8881-0.0742-0.08370.0721-0.00630.19730.2138-0.0691-0.0741-0.12310.5480.0704-0.01770.5701-0.06910.69120.1481122.7143105.4441
21.157-0.2403-0.42260.5180.17730.7661-0.0753-0.10090.1674-0.07360.10020.12130.0052-0.1755-0.02490.564-0.026-0.0810.51170.01390.704324.688116.293480.7695
31.7134-0.6857-0.02111.29840.42260.6946-0.02410.0048-0.0522-0.22020.030.2887-0.001-0.1057-0.00590.5948-0.0555-0.09460.56390.07040.482827.133191.821670.1256
41.0682-0.71670.14161.1501-0.39790.6176-0.102-0.0413-0.1129-0.03780.08850.29790.1203-0.18590.01350.5725-0.075-0.03520.56130.04940.588824.833968.632782.2048
50.87090.21610.34430.46880.27791.2857-0.1684-0.1953-0.02160.25580.13250.3003-0.0408-0.11070.03590.55250.05170.0870.54820.11030.563219.869163.545107.1392
60.91820.0450.08361.01920.4371.1863-0.1082-0.1528-0.0590.32910.15220.23870.1205-0.0957-0.04390.64270.14910.11440.68240.06420.451716.267580.9223127.136
71.26410.24430.28331.61050.26630.458-0.0609-0.29710.05350.15560.07560.2522-0.0478-0.0994-0.01470.56640.14550.0870.7178-0.0510.424316.3735107.2738126.1368
80.3771-0.3497-0.28751.19240.12120.6216-0.0167-0.05270.2159-0.14710.1573-0.2503-0.14010.1484-0.14060.535-0.07390.03120.5795-0.16220.667170.5371118.21190.0033
90.9196-0.61430.45681.321-0.38871.15240.0025-0.05410.2381-0.20120.0083-0.2554-0.0030.126-0.01080.5823-0.0190.06240.596-0.09340.502672.928893.974477.8232
100.259-0.22080.0730.3538-0.31591.1581-0.1049-0.068-0.0556-0.07160.0836-0.05050.01480.27260.02130.64850.0750.01670.679-0.04250.48470.968369.057388.6892
110.88780.21190.35870.8125-0.0711.169-0.0438-0.1835-0.14590.13450.1925-0.09740.14240.1375-0.14870.64580.2245-0.0330.6340.00070.378566.068162.3312114.7028
122.1570.60620.36041.62740.21610.3907-0.1479-0.4766-0.01820.20510.1639-0.12490.05080.033-0.0160.73890.2377-0.0920.8284-0.01250.160762.101978.7935135.8622
130.77830.5012-0.40651.422-0.46680.8162-0.0777-0.30140.08830.37060.0761-0.102-0.03650.20350.00160.71310.1485-0.15280.8514-0.23290.227661.8852106.0385136.6231
141.47890.361-0.04190.9474-0.45770.39240.0172-0.15230.35670.15260.0386-0.1493-0.0650.1099-0.05580.5810.0205-0.1150.5813-0.28180.520265.719123.6257116.1905
150.67240.0882-0.36590.7389-0.38460.5617-0.17720.1159-0.1079-0.14150.15240.0577-0.0387-0.06690.02480.81590.0484-0.01010.681-0.01360.434127.4328120.079411.5278
160.7284-0.3022-0.56250.33580.12010.9905-0.13120.1554-0.1756-0.20320.10550.19880.0116-0.13850.02570.8312-0.0381-0.03330.63910.03820.476732.3154113.6142-13.1551
170.3387-0.63260.04151.52080.21020.2843-0.03120.01290.0387-0.0862-0.0029-0.0335-0.0020.03810.03410.5033-0.0502-0.0190.439-0.03110.011734.677689.1344-23.5558
180.0279-0.14350.06611.0641-0.3220.2712-0.02170.0285-0.0335-0.05920.08940.11130.05540.0682-0.06770.47680.0027-0.02450.3901-0.07790.125532.059465.92-11.4479
190.0543-0.07540.22430.4904-0.12491.02090.0071-0.005-0.03770.02590.14310.02630.05570.0241-0.15020.4213-0.00280.00950.3471-0.00930.205426.692360.875113.4231
200.2240.45850.38360.9860.72060.8453-0.0076-0.0333-0.01630.04920.0031-0.0370.0509-0.10570.00450.4130.02740.07050.41780.03020.071922.886578.323733.3618
210.39180.6946-0.08491.2825-0.1880.0771-0.0358-0.02530.01040.08020.00850.0292-0.1024-0.00640.02730.45990.06420.04510.4354-0.03680.053823.2135104.661932.208
220.5246-0.2883-0.23661.0691-0.13370.2231-0.0946-0.01710.0581-0.07270.1163-0.1152-0.0590.0101-0.02170.5013-0.10640.06010.3835-0.050.023578.047115.1777-3.241
230.3219-0.3267-0.11440.5114-0.22410.7858-0.00860.08350.0483-0.0533-0.0566-0.1223-0.03390.06570.06520.442-0.0230.08450.4899-0.10570.069580.433490.8452-15.0983
240.348-0.6760.02831.38340.12590.80820.0210.05890.0205-0.04260.0129-0.08790.11910.1145-0.03390.42280.02960.04940.4117-0.13540.057378.047665.9928-4.2047
250.10260.0014-0.16870.7183-0.11790.34330.00520.0201-0.02450.0916-0.0067-0.05980.0890.05950.00150.49860.0943-0.04390.3104-0.09010.134872.714859.355821.6381
260.1152-0.06660.10120.34580.10510.82690.0314-0.0136-0.06080.11060.0354-0.06010.0733-0.0455-0.06680.48980.0605-0.03970.3238-0.05270.072868.533475.898142.7282
270.07680.1939-0.1450.7186-0.16970.61470.075-0.0042-0.02690.0836-0.0854-0.0544-0.2110.02010.01030.49980.0093-0.01910.3557-0.07040.032968.4718103.115343.3488
281.6868-0.0075-0.2440.80340.11960.2058-0.1094-0.09520.0168-0.04840.158-0.1068-0.10440.0356-0.04860.5122-0.0443-0.0010.326-0.05420.026272.6723120.658622.9086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 210
2X-RAY DIFFRACTION2B15 - 214
3X-RAY DIFFRACTION3C15 - 210
4X-RAY DIFFRACTION4D15 - 210
5X-RAY DIFFRACTION5E15 - 214
6X-RAY DIFFRACTION6F15 - 210
7X-RAY DIFFRACTION7G15 - 209
8X-RAY DIFFRACTION8H15 - 192
9X-RAY DIFFRACTION9I15 - 192
10X-RAY DIFFRACTION10J15 - 192
11X-RAY DIFFRACTION11K15 - 192
12X-RAY DIFFRACTION12L15 - 192
13X-RAY DIFFRACTION13M15 - 192
14X-RAY DIFFRACTION14N15 - 193
15X-RAY DIFFRACTION15a15 - 211
16X-RAY DIFFRACTION16b15 - 214
17X-RAY DIFFRACTION17c15 - 211
18X-RAY DIFFRACTION18d15 - 210
19X-RAY DIFFRACTION19e15 - 214
20X-RAY DIFFRACTION20f15 - 210
21X-RAY DIFFRACTION21g15 - 210
22X-RAY DIFFRACTION22h15 - 192
23X-RAY DIFFRACTION23i15 - 192
24X-RAY DIFFRACTION24j15 - 192
25X-RAY DIFFRACTION25k15 - 192
26X-RAY DIFFRACTION26l15 - 192
27X-RAY DIFFRACTION27m15 - 192
28X-RAY DIFFRACTION28n15 - 192

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