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- PDB-5e0s: crystal structure of the active form of the proteolytic complex c... -

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Basic information

Entry
Database: PDB / ID: 5e0s
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
KeywordsHYDROLASE
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / peptidoglycan-based cell wall / ATPase binding / serine-type endopeptidase activity / plasma membrane / cytoplasm / cytosol
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 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 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 29, 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
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 1
I: ATP-dependent Clp protease proteolytic subunit 1
J: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 1
L: ATP-dependent Clp protease proteolytic subunit 1
M: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1
a: ATP-dependent Clp protease proteolytic subunit 2
b: ATP-dependent Clp protease proteolytic subunit 2
c: ATP-dependent Clp protease proteolytic subunit 2
d: ATP-dependent Clp protease proteolytic subunit 2
e: ATP-dependent Clp protease proteolytic subunit 2
f: ATP-dependent Clp protease proteolytic subunit 2
g: ATP-dependent Clp protease proteolytic subunit 2
h: ATP-dependent Clp protease proteolytic subunit 1
i: ATP-dependent Clp protease proteolytic subunit 1
j: ATP-dependent Clp protease proteolytic subunit 1
k: ATP-dependent Clp protease proteolytic subunit 1
l: ATP-dependent Clp protease proteolytic subunit 1
m: ATP-dependent Clp protease proteolytic subunit 1
n: ATP-dependent Clp protease proteolytic subunit 1


Theoretical massNumber of molelcules
Total (without water)634,06628
Polymers634,06628
Non-polymers00
Water1,910106
1
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 1
I: ATP-dependent Clp protease proteolytic subunit 1
J: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 1
L: ATP-dependent Clp protease proteolytic subunit 1
M: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1


Theoretical massNumber of molelcules
Total (without water)317,03314
Polymers317,03314
Non-polymers00
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55480 Å2
ΔGint-240 kcal/mol
Surface area94300 Å2
MethodPISA
2
a: ATP-dependent Clp protease proteolytic subunit 2
b: ATP-dependent Clp protease proteolytic subunit 2
c: ATP-dependent Clp protease proteolytic subunit 2
d: ATP-dependent Clp protease proteolytic subunit 2
e: ATP-dependent Clp protease proteolytic subunit 2
f: ATP-dependent Clp protease proteolytic subunit 2
g: ATP-dependent Clp protease proteolytic subunit 2
h: ATP-dependent Clp protease proteolytic subunit 1
i: ATP-dependent Clp protease proteolytic subunit 1
j: ATP-dependent Clp protease proteolytic subunit 1
k: ATP-dependent Clp protease proteolytic subunit 1
l: ATP-dependent Clp protease proteolytic subunit 1
m: ATP-dependent Clp protease proteolytic subunit 1
n: ATP-dependent Clp protease proteolytic subunit 1


Theoretical massNumber of molelcules
Total (without water)317,03314
Polymers317,03314
Non-polymers00
Water23413
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55400 Å2
ΔGint-238 kcal/mol
Surface area94470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.179, 183.541, 188.373
Angle α, β, γ (deg.)90.00, 94.53, 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
1010A14 - 209
2010B14 - 209
1020A14 - 210
2020C14 - 210
1030A14 - 210
2030D14 - 210
1040A14 - 209
2040E14 - 209
1050A14 - 210
2050F14 - 210
1060A14 - 208
2060G14 - 208
1070A14 - 209
2070a14 - 209
1080A14 - 209
2080b14 - 209
1090A14 - 209
2090c14 - 209
10100A14 - 210
20100d14 - 210
10110A14 - 209
20110e14 - 209
10120A14 - 210
20120f14 - 210
10130A14 - 210
20130g14 - 210
10140B14 - 209
20140C14 - 209
10150B14 - 209
20150D14 - 209
10160B14 - 211
20160E14 - 211
10170B14 - 209
20170F14 - 209
10180B14 - 208
20180G14 - 208
10190B14 - 210
20190a14 - 210
10200B14 - 214
20200b14 - 214
10210B14 - 210
20210c14 - 210
10220B14 - 209
20220d14 - 209
10230B14 - 211
20230e14 - 211
10240B14 - 209
20240f14 - 209
10250B14 - 209
20250g14 - 209
10260C14 - 210
20260D14 - 210
10270C14 - 209
20270E14 - 209
10280C14 - 210
20280F14 - 210
10290C14 - 208
20290G14 - 208
10300C14 - 209
20300a14 - 209
10310C14 - 209
20310b14 - 209
10320C14 - 209
20320c14 - 209
10330C14 - 210
20330d14 - 210
10340C14 - 209
20340e14 - 209
10350C14 - 210
20350f14 - 210
10360C14 - 210
20360g14 - 210
10370D14 - 209
20370E14 - 209
10380D14 - 210
20380F14 - 210
10390D14 - 208
20390G14 - 208
10400D14 - 209
20400a14 - 209
10410D14 - 209
20410b14 - 209
10420D14 - 209
20420c14 - 209
10430D14 - 210
20430d14 - 210
10440D14 - 209
20440e14 - 209
10450D14 - 210
20450f14 - 210
10460D14 - 210
20460g14 - 210
10470E14 - 209
20470F14 - 209
10480E14 - 208
20480G14 - 208
10490E14 - 210
20490a14 - 210
10500E14 - 211
20500b14 - 211
10510E14 - 210
20510c14 - 210
10520E14 - 209
20520d14 - 209
10530E14 - 212
20530e14 - 212
10540E14 - 209
20540f14 - 209
10550E14 - 209
20550g14 - 209
10560F14 - 208
20560G14 - 208
10570F14 - 209
20570a14 - 209
10580F14 - 209
20580b14 - 209
10590F14 - 209
20590c14 - 209
10600F14 - 210
20600d14 - 210
10610F14 - 209
20610e14 - 209
10620F14 - 210
20620f14 - 210
10630F14 - 210
20630g14 - 210
10640G14 - 208
20640a14 - 208
10650G14 - 208
20650b14 - 208
10660G14 - 208
20660c14 - 208
10670G14 - 208
20670d14 - 208
10680G14 - 208
20680e14 - 208
10690G14 - 208
20690f14 - 208
10700G14 - 208
20700g14 - 208
10710H15 - 191
20710I15 - 191
10720H15 - 191
20720J15 - 191
10730H15 - 191
20730K15 - 191
10740H15 - 191
20740L15 - 191
10750H15 - 191
20750M15 - 191
10760H15 - 191
20760N15 - 191
10770H15 - 191
20770h15 - 191
10780H15 - 191
20780i15 - 191
10790H15 - 191
20790j15 - 191
10800H15 - 191
20800k15 - 191
10810H15 - 191
20810l15 - 191
10820H15 - 191
20820m15 - 191
10830H15 - 191
20830n15 - 191
10840I15 - 192
20840J15 - 192
10850I15 - 192
20850K15 - 192
10860I15 - 192
20860L15 - 192
10870I15 - 192
20870M15 - 192
10880I15 - 191
20880N15 - 191
10890I15 - 191
20890h15 - 191
10900I15 - 191
20900i15 - 191
10910I15 - 192
20910j15 - 192
10920I15 - 192
20920k15 - 192
10930I15 - 192
20930l15 - 192
10940I15 - 192
20940m15 - 192
10950I15 - 191
20950n15 - 191
10960J15 - 192
20960K15 - 192
10970J15 - 192
20970L15 - 192
10980J15 - 192
20980M15 - 192
10990J15 - 191
20990N15 - 191
101000J15 - 191
201000h15 - 191
101010J15 - 191
201010i15 - 191
101020J15 - 192
201020j15 - 192
101030J15 - 192
201030k15 - 192
101040J15 - 192
201040l15 - 192
101050J15 - 192
201050m15 - 192
101060J15 - 191
201060n15 - 191
101070K15 - 192
201070L15 - 192
101080K15 - 192
201080M15 - 192
101090K15 - 191
201090N15 - 191
101100K15 - 191
201100h15 - 191
101110K15 - 191
201110i15 - 191
101120K15 - 192
201120j15 - 192
101130K15 - 192
201130k15 - 192
101140K15 - 192
201140l15 - 192
101150K15 - 192
201150m15 - 192
101160K15 - 191
201160n15 - 191
101170L15 - 192
201170M15 - 192
101180L15 - 191
201180N15 - 191
101190L15 - 191
201190h15 - 191
101200L15 - 191
201200i15 - 191
101210L15 - 192
201210j15 - 192
101220L15 - 192
201220k15 - 192
101230L15 - 192
201230l15 - 192
101240L15 - 192
201240m15 - 192
101250L15 - 191
201250n15 - 191
101260M15 - 191
201260N15 - 191
101270M15 - 191
201270h15 - 191
101280M15 - 191
201280i15 - 191
101290M15 - 192
201290j15 - 192
101300M15 - 192
201300k15 - 192
101310M15 - 192
201310l15 - 192
101320M15 - 192
201320m15 - 192
101330M15 - 191
201330n15 - 191
101340N15 - 196
201340h15 - 196
101350N15 - 194
201350i15 - 194
101360N15 - 191
201360j15 - 191
101370N15 - 191
201370k15 - 191
101380N15 - 191
201380l15 - 191
101390N15 - 191
201390m15 - 191
101400N15 - 198
201400n15 - 198
101410a14 - 210
201410b14 - 210
101420a14 - 211
201420c14 - 211
101430a14 - 209
201430d14 - 209
101440a14 - 210
201440e14 - 210
101450a14 - 209
201450f14 - 209
101460a14 - 209
201460g14 - 209
101470b14 - 210
201470c14 - 210
101480b14 - 209
201480d14 - 209
101490b14 - 211
201490e14 - 211
101500b14 - 209
201500f14 - 209
101510b14 - 209
201510g14 - 209
101520c14 - 209
201520d14 - 209
101530c14 - 210
201530e14 - 210
101540c14 - 209
201540f14 - 209
101550c14 - 209
201550g14 - 209
101560d14 - 209
201560e14 - 209
101570d14 - 210
201570f14 - 210
101580d14 - 210
201580g14 - 210
101590e14 - 209
201590f14 - 209
101600e14 - 209
201600g14 - 209
101610f14 - 210
201610g14 - 210
101620h15 - 194
201620i15 - 194
101630h15 - 191
201630j15 - 191
101640h15 - 191
201640k15 - 191
101650h15 - 191
201650l15 - 191
101660h15 - 191
201660m15 - 191
101670h15 - 196
201670n15 - 196
101680i15 - 191
201680j15 - 191
101690i15 - 191
201690k15 - 191
101700i15 - 191
201700l15 - 191
101710i15 - 191
201710m15 - 191
101720i15 - 194
201720n15 - 194
101730j15 - 192
201730k15 - 192
101740j15 - 192
201740l15 - 192
101750j15 - 192
201750m15 - 192
101760j15 - 191
201760n15 - 191
101770k15 - 192
201770l15 - 192
101780k15 - 192
201780m15 - 192
101790k15 - 191
201790n15 - 191
101800l15 - 192
201800m15 - 192
101810l15 - 191
201810n15 - 191
101820m15 - 191
201820n15 - 191

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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
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

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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
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.9 %
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, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.877→50 Å / Num. obs: 147557 / % possible obs: 94.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.1
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.8 / % possible all: 84.9

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.9→49.27 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 37.18 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23585 4469 3 %RANDOM
Rwork0.20404 ---
obs0.20499 143061 93.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.184 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-3.79 Å2
2---4.25 Å20 Å2
3---4.82 Å2
Refinement stepCycle: 1 / Resolution: 2.9→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40564 0 0 106 40670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01941184
X-RAY DIFFRACTIONr_bond_other_d0.0080.0239871
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.97255695
X-RAY DIFFRACTIONr_angle_other_deg2.2391596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52255263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69324.1591808
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.708157177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.29515295
X-RAY DIFFRACTIONr_chiral_restr0.0920.26442
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0246732
X-RAY DIFFRACTIONr_gen_planes_other0.0070.029011
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)
11A117060.06
12B117060.06
21A115940.08
22C115940.08
31A116450.08
32D116450.08
41A116580.07
42E116580.07
51A115900.08
52F115900.08
61A115990.07
62G115990.07
71A117060.07
72a117060.07
81A116080.07
82b116080.07
91A115590.08
92c115590.08
101A116170.07
102d116170.07
111A115220.08
112e115220.08
121A117350.06
122f117350.06
131A116940.07
132g116940.07
141B115350.08
142C115350.08
151B116010.07
152D116010.07
161B116560.07
162E116560.07
171B114970.08
172F114970.08
181B115370.06
182G115370.06
191B116480.07
192a116480.07
201B116100.08
202b116100.08
211B116360.07
212c116360.07
221B115830.07
222d115830.07
231B115580.07
232e115580.07
241B116060.07
242f116060.07
251B116110.07
252g116110.07
261C115980.08
262D115980.08
271C116610.08
272E116610.08
281C115430.08
282F115430.08
291C115630.07
292G115630.07
301C115740.08
302a115740.08
311C115320.08
312b115320.08
321C115530.07
322c115530.07
331C115480.08
332d115480.08
341C114580.08
342e114580.08
351C117060.07
352f117060.07
361C116730.08
362g116730.08
371D117270.07
372E117270.07
381D116670.09
382F116670.09
391D115790.07
392G115790.07
401D116010.07
402a116010.07
411D115430.08
412b115430.08
421D116400.07
422c116400.07
431D117660.07
432d117660.07
441D116820.07
442e116820.07
451D117310.07
452f117310.07
461D116860.08
462g116860.08
471E115140.09
472F115140.09
481E117260.06
482G117260.06
491E118520.05
492a118520.05
501E116370.08
502b116370.08
511E117290.06
512c117290.06
521E116010.07
522d116010.07
531E117820.06
532e117820.06
541E117870.06
542f117870.06
551E117610.06
552g117610.06
561F114810.08
562G114810.08
571F114770.09
572a114770.09
581F114460.09
582b114460.09
591F115310.08
592c115310.08
601F116520.08
602d116520.08
611F115790.08
612e115790.08
621F117040.07
622f117040.07
631F115640.09
632g115640.09
641G116480.06
642a116480.06
651G115520.07
652b115520.07
661G115970.06
662c115970.06
671G115130.07
672d115130.07
681G115570.07
682e115570.07
691G117180.06
692f117180.06
701G116530.06
702g116530.06
711H103550.08
712I103550.08
721H104660.07
722J104660.07
731H102950.09
732K102950.09
741H103940.07
742L103940.07
751H103060.09
752M103060.09
761H103040.09
762N103040.09
771H103820.07
772h103820.07
781H103970.08
782i103970.08
791H103490.08
792j103490.08
801H103710.08
802k103710.08
811H104350.07
812l104350.07
821H104410.07
822m104410.07
831H102050.09
832n102050.09
841I104660.07
842J104660.07
851I102810.08
852K102810.08
861I103900.08
862L103900.08
871I104990.07
872M104990.07
881I104090.07
882N104090.07
891I102860.07
892h102860.07
901I104750.07
902i104750.07
911I105520.07
912j105520.07
921I103270.08
922k103270.08
931I104970.07
932l104970.07
941I104550.07
942m104550.07
951I102800.09
952n102800.09
961J103220.08
962K103220.08
971J104590.07
972L104590.07
981J104790.07
982M104790.07
991J103760.07
992N103760.07
1001J104030.06
1002h104030.06
1011J105400.06
1012i105400.06
1021J104800.06
1022j104800.06
1031J103980.07
1032k103980.07
1041J105640.06
1042l105640.06
1051J105630.06
1052m105630.06
1061J102760.08
1062n102760.08
1071K105120.07
1072L105120.07
1081K102670.09
1082M102670.09
1091K102360.08
1092N102360.08
1101K104710.07
1102h104710.07
1111K102960.08
1112i102960.08
1121K102700.08
1122j102700.08
1131K104800.07
1132k104800.07
1141K103650.08
1142l103650.08
1151K104060.08
1152m104060.08
1161K103230.08
1162n103230.08
1171L104080.08
1172M104080.08
1181L103410.08
1182N103410.08
1191L104810.07
1192h104810.07
1201L104640.07
1202i104640.07
1211L103990.08
1212j103990.08
1221L104670.07
1222k104670.07
1231L104280.07
1232l104280.07
1241L104700.07
1242m104700.07
1251L104310.07
1252n104310.07
1261M103780.07
1262N103780.07
1271M103080.08
1272h103080.08
1281M104340.07
1282i104340.07
1291M104600.08
1292j104600.08
1301M103090.08
1302k103090.08
1311M105270.07
1312l105270.07
1321M104820.07
1322m104820.07
1331M103560.07
1332n103560.07
1341N104600.08
1342h104600.08
1351N104870.08
1352i104870.08
1361N104550.07
1362j104550.07
1371N103410.07
1372k103410.07
1381N103460.07
1382l103460.07
1391N104080.07
1392m104080.07
1401N105130.1
1402n105130.1
1411a116440.07
1412b116440.07
1421a116570.07
1422c116570.07
1431a115800.08
1432d115800.08
1441a116140.07
1442e116140.07
1451a117680.06
1452f117680.06
1461a116910.06
1462g116910.06
1471b115270.08
1472c115270.08
1481b116030.07
1482d116030.07
1491b115860.08
1492e115860.08
1501b116430.07
1502f116430.07
1511b116740.07
1512g116740.07
1521c115110.08
1522d115110.08
1531c116800.06
1532e116800.06
1541c116640.07
1542f116640.07
1551c116530.07
1552g116530.07
1561d116330.08
1562e116330.08
1571d116520.07
1572f116520.07
1581d116040.07
1582g116040.07
1591e116090.07
1592f116090.07
1601e116250.07
1602g116250.07
1611f118180.07
1612g118180.07
1621h104870.08
1622i104870.08
1631h102780.08
1632j102780.08
1641h105320.06
1642k105320.06
1651h103640.07
1652l103640.07
1661h104670.06
1662m104670.06
1671h104720.09
1672n104720.09
1681i103740.08
1682j103740.08
1691i102680.08
1692k102680.08
1701i104010.07
1702l104010.07
1711i105030.07
1712m105030.07
1721i104140.09
1722n104140.09
1731j104480.06
1732k104480.06
1741j105470.06
1742l105470.06
1751j104550.07
1752m104550.07
1761j103790.07
1762n103790.07
1771k104230.07
1772l104230.07
1781k103740.07
1782m103740.07
1791k103610.07
1792n103610.07
1801l104740.07
1802m104740.07
1811l103400.07
1812n103400.07
1821m102350.08
1822n102350.08
LS refinement shellResolution: 2.877→2.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 251 -
Rwork0.347 8461 -
obs--75.2 %
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)
11.12840.4295-0.26841.0279-0.39840.6848-0.0174-0.07890.09120.11740.13780.1653-0.0974-0.1004-0.12040.2050.05920.07520.3496-0.05730.372319.9259122.4031105.4563
22.1633-0.2064-0.97510.23870.341.3088-0.0103-0.05850.102-0.12280.0620.1254-0.1074-0.131-0.05170.2154-0.0025-0.01220.29370.05310.370324.3957116.034380.917
32.3752-1.0862-0.09481.99390.56070.5562-0.0363-0.0354-0.1043-0.33180.04540.3498-0.0209-0.0881-0.00910.2326-0.0489-0.07160.35540.06750.221726.827491.751170.2927
41.5451-0.78980.11291.3226-0.53250.3379-0.1455-0.1069-0.0035-0.11940.14340.26640.1487-0.10540.00210.2435-0.05870.00180.38750.04060.340724.579668.671782.2018
51.8336-0.21490.82350.4951-0.42481.8248-0.1852-0.1895-0.04670.19210.12380.27710.2229-0.10040.06140.25670.06070.17550.30770.08670.327119.668463.6821107.177
61.83670.09151.02041.2020.87531.4011-0.1599-0.1924-0.0690.4370.14920.26410.1198-0.0740.01070.2970.14350.24370.50450.09690.228416.059980.7538126.8945
71.46460.41870.03372.09720.08410.0878-0.1126-0.21350.07590.30180.1460.3297-0.1135-0.0095-0.03340.28590.13130.16080.5004-0.02090.167216.1579106.973125.9745
80.3642-0.29830.08581.2672-0.02570.9820.0621-0.08550.2869-0.12340.1008-0.3164-0.10160.1456-0.16290.2116-0.07020.07850.3461-0.20210.333270.6816116.880790.7725
90.8895-0.23020.67481.5722-0.10690.95070.0414-0.08260.2237-0.14790.0062-0.3357-0.04110.1557-0.04760.2672-0.03870.11940.3951-0.12540.245372.406793.863177.8701
100.6152-0.11990.31251.3935-0.34321.2958-0.1033-0.13570.0011-0.05490.1452-0.11990.01830.269-0.04190.26190.08590.09620.4525-0.07280.187670.476468.971688.6604
111.1040.49580.38661.23720.3121.4309-0.0677-0.1312-0.15220.21260.1462-0.11180.19120.2008-0.07850.31150.24890.03850.4659-0.02260.050865.591762.2205114.6156
121.58620.39730.01562.02690.5480.3223-0.1283-0.38080.01710.2510.1305-0.11050.10230.0743-0.00220.4880.233-0.02960.6791-0.04630.014161.587378.5535135.8209
131.0713-0.1556-0.78751.6744-0.43330.90710.0058-0.29120.18940.3560.1082-0.1303-0.03450.1957-0.1140.48470.1383-0.09170.6786-0.21530.088961.3842105.7479136.6868
141.58650.0011-0.34411.3206-0.27550.68210.0249-0.23880.25280.16590.1171-0.2206-0.0160.1434-0.1420.3132-0.0019-0.03820.4054-0.26660.234265.5873123.6331115.9596
150.4679-0.21390.3780.91640.25780.89720.01070.09630.0487-0.1250.0442-0.2271-0.20760.2224-0.05490.2472-0.12370.16870.3596-0.04260.271378.0507115.0168-3.5228
160.20240.22710.30831.5247-0.18250.7943-0.01140.1501-0.0065-0.1629-0.0017-0.2811-0.09280.26710.01310.2149-0.0320.20440.4672-0.14050.266180.369290.5741-15.1457
170.2115-0.19450.20911.4837-0.50981.3671-0.00690.1266-0.0618-0.12620.0498-0.25050.09040.2892-0.04290.19560.07410.16230.3609-0.17740.331977.696166.0402-4.1623
180.67860.4951-0.13270.65830.28460.94360.02070.0001-0.03170.10810.0048-0.1610.09210.1378-0.02550.31340.13190.01110.2939-0.09990.366572.364559.368321.614
190.8544-0.0042-0.36220.7478-0.02760.60370.0684-0.0863-0.10010.1364-0.0081-0.20890.07460.1181-0.06020.32690.0886-0.00760.302-0.0860.22768.204875.818442.7176
200.7093-0.2934-0.40321.1576-0.20381.11730.0713-0.10180.04920.1475-0.0227-0.1355-0.13940.1227-0.04860.31360.03010.02210.3173-0.10.135968.1325103.088743.3624
210.8661-0.4302-0.050.6469-0.07360.9972-0.0457-0.06260.13590.06730.0619-0.1339-0.05760.1806-0.01620.3282-0.07150.04750.3159-0.07120.283472.853120.94922.5543
220.67030.2007-0.30390.5443-0.28720.5611-0.09710.07590.01330.0820.13780.0457-0.145-0.0669-0.04070.10070.0130.01470.05360.00760.005827.3455119.928811.5355
232.3919-0.1095-0.780.22550.26311.4038-0.04990.1728-0.1388-0.2262-0.00350.1344-0.1467-0.1170.05340.3287-0.0366-0.01080.2540.03010.311332.2095113.5398-13.0381
241.1524-0.51710.15191.93660.58820.3556-0.0591-0.0222-0.0789-0.32790.02260.1873-0.02040.00450.03660.2956-0.03080.03060.3658-0.00430.17934.554789.2273-23.3754
250.6652-0.13280.04321.1989-0.17280.0716-0.02510.0154-0.0782-0.14580.10760.18170.1042-0.0225-0.08260.2798-0.0060.01080.3515-0.08630.312531.937366.1246-11.4046
261.0091-0.34750.82960.2188-0.50991.8989-0.0086-0.127-0.02880.07270.09120.09180.1819-0.1522-0.08250.25580.00360.05710.2845-0.03470.435326.616161.198213.4861
271.59210.09410.8950.66690.80861.5691-0.0111-0.09880.03610.20090.01310.13730.0948-0.1698-0.0020.20920.00470.1260.37690.04330.289922.812978.398133.1053
281.70630.45210.7121.66990.22750.3965-0.0785-0.03880.07810.20380.08950.2368-0.1526-0.1466-0.01090.25560.06750.11530.4292-0.01060.232223.147104.589532.0458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 210
2X-RAY DIFFRACTION2B14 - 214
3X-RAY DIFFRACTION3C14 - 210
4X-RAY DIFFRACTION4D14 - 210
5X-RAY DIFFRACTION5E14 - 212
6X-RAY DIFFRACTION6F14 - 210
7X-RAY DIFFRACTION7G14 - 209
8X-RAY DIFFRACTION8H7 - 192
9X-RAY DIFFRACTION9I15 - 192
10X-RAY DIFFRACTION10J15 - 192
11X-RAY DIFFRACTION11K15 - 192
12X-RAY DIFFRACTION12L15 - 192
13X-RAY DIFFRACTION13M15 - 192
14X-RAY DIFFRACTION14N15 - 198
15X-RAY DIFFRACTION15h15 - 197
16X-RAY DIFFRACTION16i15 - 195
17X-RAY DIFFRACTION17j15 - 192
18X-RAY DIFFRACTION18k15 - 192
19X-RAY DIFFRACTION19l15 - 192
20X-RAY DIFFRACTION20m15 - 192
21X-RAY DIFFRACTION21n15 - 198
22X-RAY DIFFRACTION22a14 - 211
23X-RAY DIFFRACTION23b14 - 214
24X-RAY DIFFRACTION24c14 - 211
25X-RAY DIFFRACTION25d14 - 210
26X-RAY DIFFRACTION26e14 - 212
27X-RAY DIFFRACTION27f14 - 210
28X-RAY DIFFRACTION28g14 - 210

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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