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- PDB-6qx2: 3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA -

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Basic information

Entry
Database: PDB / ID: 6qx2
Title3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA
Components
  • (DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)- ...) x 3
  • (DNA gyrase subunit ...) x 9
KeywordsISOMERASE / Inhibitor / DNA complex
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A ...DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-JK8 / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit B / DNA gyrase subunit B / DNA gyrase subunit B / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBax, B.D.
Funding support1items
OrganizationGrant numberCountry
European Union115583
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.
Authors: Thalji, R.K. / Raha, K. / Andreotti, D. / Checchia, A. / Cui, H. / Meneghelli, G. / Profeta, R. / Tonelli, F. / Tommasi, S. / Bakshi, T. / Donovan, B.T. / Howells, A. / Jain, S. / Nixon, C. ...Authors: Thalji, R.K. / Raha, K. / Andreotti, D. / Checchia, A. / Cui, H. / Meneghelli, G. / Profeta, R. / Tonelli, F. / Tommasi, S. / Bakshi, T. / Donovan, B.T. / Howells, A. / Jain, S. / Nixon, C. / Quinque, G. / McCloskey, L. / Bax, B.D. / Neu, M. / Chan, P.F. / Stavenger, R.A.
History
DepositionMar 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA gyrase subunit B,DNA gyrase subunit B
A: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
E: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
K: DNA gyrase subunit B,DNA gyrase subunit B
J: DNA gyrase subunit A
M: DNA gyrase subunit B,DNA gyrase subunit B
L: DNA gyrase subunit A
N: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
O: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
S: DNA gyrase subunit B,DNA gyrase subunit B
R: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
V: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
W: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
b: DNA gyrase subunit B,DNA gyrase subunit B
a: DNA gyrase subunit A
d: DNA gyrase subunit B,DNA gyrase subunit B
c: DNA gyrase subunit A
e: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
f: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
k: DNA gyrase subunit B,DNA gyrase subunit B
j: DNA gyrase subunit A
m: DNA gyrase subunit B,DNA gyrase subunit B
l: DNA gyrase subunit A
n: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
o: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
s: DNA gyrase subunit B,DNA gyrase subunit B
r: DNA gyrase subunit A
u: DNA gyrase subunit B,DNA gyrase subunit B
t: DNA gyrase subunit A
v: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
w: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)993,37548
Polymers988,99736
Non-polymers4,37812
Water0
1
B: DNA gyrase subunit B,DNA gyrase subunit B
A: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
E: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0648
Polymers165,3346
Non-polymers7302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19190 Å2
ΔGint-104 kcal/mol
Surface area55710 Å2
MethodPISA
2
K: DNA gyrase subunit B,DNA gyrase subunit B
J: DNA gyrase subunit A
M: DNA gyrase subunit B,DNA gyrase subunit B
L: DNA gyrase subunit A
N: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
O: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,2238
Polymers164,4936
Non-polymers7302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19370 Å2
ΔGint-102 kcal/mol
Surface area55710 Å2
MethodPISA
3
S: DNA gyrase subunit B,DNA gyrase subunit B
R: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
V: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
W: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,7608
Polymers165,0306
Non-polymers7302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19890 Å2
ΔGint-104 kcal/mol
Surface area55580 Å2
MethodPISA
4
b: DNA gyrase subunit B,DNA gyrase subunit B
a: DNA gyrase subunit A
d: DNA gyrase subunit B,DNA gyrase subunit B
c: DNA gyrase subunit A
e: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
f: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,3698
Polymers163,6406
Non-polymers7302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19000 Å2
ΔGint-105 kcal/mol
Surface area55570 Å2
MethodPISA
5
k: DNA gyrase subunit B,DNA gyrase subunit B
j: DNA gyrase subunit A
m: DNA gyrase subunit B,DNA gyrase subunit B
l: DNA gyrase subunit A
n: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
o: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,9948
Polymers165,2646
Non-polymers7302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19570 Å2
ΔGint-103 kcal/mol
Surface area55850 Å2
MethodPISA
6
s: DNA gyrase subunit B,DNA gyrase subunit B
r: DNA gyrase subunit A
u: DNA gyrase subunit B,DNA gyrase subunit B
t: DNA gyrase subunit A
v: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
w: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,9658
Polymers165,2356
Non-polymers7302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20100 Å2
ΔGint-100 kcal/mol
Surface area55160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.640, 410.120, 93.940
Angle α, β, γ (deg.)90.00, 120.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12B
22K
13B
23M
14B
24S
15B
25U
16B
26b
17B
27d
18B
28k
19B
29m
110B
210s
111B
211u
112A
212C
113A
213J
114A
214L
115A
215R
116A
216T
117A
217a
118A
218c
119A
219j
120A
220l
121A
221r
122A
222t
123D
223K
124D
224M
125D
225S
126D
226U
127D
227b
128D
228d
129D
229k
130D
230m
131D
231s
132D
232u
133C
233J
134C
234L
135C
235R
136C
236T
137C
237a
138C
238c
139C
239j
140C
240l
141C
241r
142C
242t
143E
243F
144E
244N
145E
245O
146E
246V
147E
247W
148E
248e
149E
249f
150E
250n
151E
251o
152E
252v
153E
253w
154F
254N
155F
255O
156F
256V
157F
257W
158F
258e
159F
259f
160F
260n
161F
261o
162F
262v
163F
263w
164K
264M
165K
265S
166K
266U
167K
267b
168K
268d
169K
269k
170K
270m
171K
271s
172K
272u
173J
273L
174J
274R
175J
275T
176J
276a
177J
277c
178J
278j
179J
279l
180J
280r
181J
281t
182M
282S
183M
283U
184M
284b
185M
285d
186M
286k
187M
287m
188M
288s
189M
289u
190L
290R
191L
291T
192L
292a
193L
293c
194L
294j
195L
295l
196L
296r
197L
297t
198N
298O
199N
299V
1100N
2100W
1101N
2101e
1102N
2102f
1103N
2103n
1104N
2104o
1105N
2105v
1106N
2106w
1107O
2107V
1108O
2108W
1109O
2109e
1110O
2110f
1111O
2111n
1112O
2112o
1113O
2113v
1114O
2114w
1115S
2115U
1116S
2116b
1117S
2117d
1118S
2118k
1119S
2119m
1120S
2120s
1121S
2121u
1122R
2122T
1123R
2123a
1124R
2124c
1125R
2125j
1126R
2126l
1127R
2127r
1128R
2128t
1129U
2129b
1130U
2130d
1131U
2131k
1132U
2132m
1133U
2133s
1134U
2134u
1135T
2135a
1136T
2136c
1137T
2137j
1138T
2138l
1139T
2139r
1140T
2140t
1141V
2141W
1142V
2142e
1143V
2143f
1144V
2144n
1145V
2145o
1146V
2146v
1147V
2147w
1148W
2148e
1149W
2149f
1150W
2150n
1151W
2151o
1152W
2152v
1153W
2153w
1154b
2154d
1155b
2155k
1156b
2156m
1157b
2157s
1158b
2158u
1159a
2159c
1160a
2160j
1161a
2161l
1162a
2162r
1163a
2163t
1164d
2164k
1165d
2165m
1166d
2166s
1167d
2167u
1168c
2168j
1169c
2169l
1170c
2170r
1171c
2171t
1172e
2172f
1173e
2173n
1174e
2174o
1175e
2175v
1176e
2176w
1177f
2177n
1178f
2178o
1179f
2179v
1180f
2180w
1181k
2181m
1182k
2182s
1183k
2183u
1184j
2184l
1185j
2185r
1186j
2186t
1187m
2187s
1188m
2188u
1189l
2189r
1190l
2190t
1191n
2191o
1192n
2192v
1193n
2193w
1194o
2194v
1195o
2195w
1196s
2196u
1197r
2197t
1198v
2198w

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSVALVALBA417 - 6382 - 186
21LYSLYSVALVALDC417 - 6381 - 188
12LYSLYSALAALABA417 - 6372 - 185
22LYSLYSALAALAKG417 - 6372 - 185
13LYSLYSVALVALBA417 - 6382 - 186
23LYSLYSVALVALMI417 - 6381 - 188
14LYSLYSVALVALBA417 - 6382 - 186
24LYSLYSVALVALSM417 - 6382 - 186
15LYSLYSVALVALBA417 - 6382 - 186
25LYSLYSVALVALUO417 - 6381 - 188
16LYSLYSVALVALBA417 - 6382 - 186
26LYSLYSVALVALbS417 - 6382 - 186
17LYSLYSALAALABA417 - 6372 - 185
27LYSLYSALAALAdU417 - 6371 - 181
18LYSLYSALAALABA417 - 6372 - 185
28LYSLYSALAALAkY417 - 6372 - 185
19LYSLYSVALVALBA417 - 6382 - 186
29LYSLYSVALVALmAA417 - 6381 - 188
110LYSLYSALAALABA417 - 6372 - 185
210LYSLYSALAALAsEA417 - 6372 - 185
111LYSLYSALAALABA417 - 6372 - 185
211LYSLYSALAALAuGA417 - 6371 - 187
112GLUGLUGLNGLNAB11 - 48910 - 488
212GLUGLUGLNGLNCD11 - 48910 - 488
113GLUGLUGLYGLYAB11 - 49110 - 490
213GLUGLUGLYGLYJH11 - 4911 - 480
114GLUGLULEULEUAB11 - 49010 - 489
214GLUGLULEULEULJ11 - 49010 - 489
115GLUGLUGLYGLYAB11 - 49110 - 490
215GLUGLUGLYGLYRN11 - 49110 - 490
116GLUGLULEULEUAB11 - 49010 - 489
216GLUGLULEULEUTP11 - 49010 - 489
117GLUGLUGLYGLYAB11 - 49110 - 490
217GLUGLUGLYGLYaT11 - 49110 - 490
118GLUGLUGLNGLNAB11 - 48910 - 488
218GLUGLUGLNGLNcV11 - 48910 - 488
119GLUGLUGLYGLYAB11 - 49110 - 490
219GLUGLUGLYGLYjZ11 - 49110 - 490
120GLUGLULEULEUAB11 - 49010 - 489
220GLUGLULEULEUlBA11 - 49010 - 489
121GLUGLULEULEUAB11 - 49010 - 489
221GLUGLULEULEUrFA11 - 49010 - 489
122GLUGLULEULEUAB11 - 49010 - 489
222GLUGLULEULEUtHA11 - 49010 - 489
123LYSLYSVALVALDC417 - 6381 - 188
223LYSLYSVALVALKG417 - 6382 - 186
124LYSLYSALAALADC417 - 6371 - 187
224LYSLYSALAALAMI417 - 6371 - 187
125LYSLYSVALVALDC417 - 6381 - 188
225LYSLYSVALVALSM417 - 6382 - 186
126LYSLYSVALVALDC417 - 6381 - 188
226LYSLYSVALVALUO417 - 6381 - 188
127LYSLYSVALVALDC417 - 6381 - 188
227LYSLYSVALVALbS417 - 6382 - 186
128LYSLYSALAALADC417 - 6371 - 187
228LYSLYSALAALAdU417 - 6371 - 181
129LYSLYSVALVALDC417 - 6381 - 188
229LYSLYSVALVALkY417 - 6382 - 186
130LYSLYSVALVALDC417 - 6381 - 188
230LYSLYSVALVALmAA417 - 6381 - 188
131LYSLYSVALVALDC417 - 6381 - 188
231LYSLYSVALVALsEA417 - 6382 - 186
132LYSLYSASNASNDC417 - 6361 - 186
232LYSLYSASNASNuGA417 - 6361 - 186
133GLUGLUGLNGLNCD11 - 48910 - 488
233GLUGLUGLNGLNJH11 - 4891 - 478
134ASNASNGLNGLNCD10 - 4899 - 488
234ASNASNGLNGLNLJ10 - 4899 - 488
135ASNASNGLNGLNCD10 - 4899 - 488
235ASNASNGLNGLNRN10 - 4899 - 488
136ASNASNGLNGLNCD10 - 4899 - 488
236ASNASNGLNGLNTP10 - 4899 - 488
137GLUGLUGLNGLNCD11 - 48910 - 488
237GLUGLUGLNGLNaT11 - 48910 - 488
138ILEILELEULEUCD9 - 4908 - 489
238ILEILELEULEUcV9 - 4908 - 489
139ASNASNGLNGLNCD10 - 4899 - 488
239ASNASNGLNGLNjZ10 - 4899 - 488
140ASNASNGLNGLNCD10 - 4899 - 488
240ASNASNGLNGLNlBA10 - 4899 - 488
141ILEILEGLNGLNCD9 - 4898 - 488
241ILEILEGLNGLNrFA9 - 4898 - 488
142ASNASNGLNGLNCD10 - 4899 - 488
242ASNASNGLNGLNtHA10 - 4899 - 488
143DGDGDTDTEE1 - 201 - 20
243DGDGDTDTFF1 - 20201 - 20
144DGDGDTDTEE1 - 201 - 20
244DGDGDTDTNK1 - 20201 - 20
145DGDGDTDTEE1 - 201 - 20
245DGDGDTDTOL1 - 201 - 20
146DGDGDCDCEE1 - 181 - 18
246DGDGDCDCVQ1 - 20181 - 18
147DGDGDTDTEE1 - 201 - 20
247DGDGDTDTWR1 - 20201 - 20
148DGDGDTDTEE1 - 201 - 20
248DGDGDTDTeW1 - 201 - 20
149DGDGDCDCEE3 - 183 - 18
249DGDGDCDCfX3 - 181 - 16
150DGDGDTDTEE1 - 201 - 20
250DGDGDTDTnCA1 - 20201 - 20
151DADADCDCEE2 - 182 - 18
251DADADCDCoDA2 - 20182 - 18
152DADADTDTEE2 - 192 - 19
252DADADTDTvIA2 - 20192 - 19
153DGDGDTDTEE1 - 201 - 20
253DGDGDTDTwJA1 - 20201 - 20
154DGDGDTDTFF1 - 20201 - 20
254DGDGDTDTNK1 - 20201 - 20
155DGDGDTDTFF1 - 20201 - 20
255DGDGDTDTOL1 - 201 - 20
156DGDGDCDCFF1 - 20181 - 18
256DGDGDCDCVQ1 - 20181 - 18
157DGDGDTDTFF1 - 20201 - 20
257DGDGDTDTWR1 - 20201 - 20
158DGDGDTDTFF1 - 20201 - 20
258DGDGDTDTeW1 - 201 - 20
159DGDGDCDCFF3 - 20183 - 18
259DGDGDCDCfX3 - 181 - 16
160DGDGDTDTFF1 - 20201 - 20
260DGDGDTDTnCA1 - 20201 - 20
161DADADCDCFF2 - 20182 - 18
261DADADCDCoDA2 - 20182 - 18
162DADADTDTFF2 - 20192 - 19
262DADADTDTvIA2 - 20192 - 19
163DGDGDTDTFF1 - 20201 - 20
263DGDGDTDTwJA1 - 20201 - 20
164LYSLYSTYRTYRKG417 - 6392 - 187
264LYSLYSTYRTYRMI417 - 6391 - 189
165LYSLYSALAALAKG417 - 6372 - 185
265LYSLYSALAALASM417 - 6372 - 185
166LYSLYSVALVALKG417 - 6382 - 186
266LYSLYSVALVALUO417 - 6381 - 188
167LYSLYSALAALAKG417 - 6372 - 185
267LYSLYSALAALAbS417 - 6372 - 185
168LYSLYSALAALAKG417 - 6372 - 185
268LYSLYSALAALAdU417 - 6371 - 181
169GLYGLYVALVALKG416 - 6381 - 186
269GLYGLYVALVALkY416 - 6381 - 186
170LYSLYSVALVALKG417 - 6382 - 186
270LYSLYSVALVALmAA417 - 6381 - 188
171GLYGLYALAALAKG416 - 6371 - 185
271GLYGLYALAALAsEA416 - 6371 - 185
172LYSLYSALAALAKG417 - 6372 - 185
272LYSLYSALAALAuGA417 - 6371 - 187
173GLUGLUGLNGLNJH11 - 4891 - 478
273GLUGLUGLNGLNLJ11 - 48910 - 488
174GLUGLUGLYGLYJH11 - 4911 - 480
274GLUGLUGLYGLYRN11 - 49110 - 490
175GLUGLUGLNGLNJH11 - 4891 - 478
275GLUGLUGLNGLNTP11 - 48910 - 488
176GLUGLUGLYGLYJH11 - 4911 - 480
276GLUGLUGLYGLYaT11 - 49110 - 490
177GLUGLUGLNGLNJH11 - 4891 - 478
277GLUGLUGLNGLNcV11 - 48910 - 488
178GLUGLUGLYGLYJH11 - 4911 - 480
278GLUGLUGLYGLYjZ11 - 49110 - 490
179GLUGLUGLNGLNJH11 - 4891 - 478
279GLUGLUGLNGLNlBA11 - 48910 - 488
180GLUGLULEULEUJH11 - 4901 - 479
280GLUGLULEULEUrFA11 - 49010 - 489
181GLUGLUGLNGLNJH11 - 4891 - 478
281GLUGLUGLNGLNtHA11 - 48910 - 488
182LYSLYSVALVALMI417 - 6381 - 188
282LYSLYSVALVALSM417 - 6382 - 186
183LYSLYSALAALAMI417 - 6371 - 187
283LYSLYSALAALAUO417 - 6371 - 187
184LYSLYSVALVALMI417 - 6381 - 188
284LYSLYSVALVALbS417 - 6382 - 186
185LYSLYSALAALAMI417 - 6371 - 187
285LYSLYSALAALAdU417 - 6371 - 181
186LYSLYSTYRTYRMI417 - 6391 - 189
286LYSLYSTYRTYRkY417 - 6392 - 187
187LYSLYSALAALAMI417 - 6371 - 187
287LYSLYSALAALAmAA417 - 6371 - 187
188LYSLYSVALVALMI417 - 6381 - 188
288LYSLYSVALVALsEA417 - 6382 - 186
189LYSLYSASNASNMI417 - 6361 - 186
289LYSLYSASNASNuGA417 - 6361 - 186
190ASNASNGLNGLNLJ10 - 4899 - 488
290ASNASNGLNGLNRN10 - 4899 - 488
191ASNASNLEULEULJ10 - 4909 - 489
291ASNASNLEULEUTP10 - 4909 - 489
192GLUGLUGLNGLNLJ11 - 48910 - 488
292GLUGLUGLNGLNaT11 - 48910 - 488
193ASNASNGLNGLNLJ10 - 4899 - 488
293ASNASNGLNGLNcV10 - 4899 - 488
194ASNASNGLNGLNLJ10 - 4899 - 488
294ASNASNGLNGLNjZ10 - 4899 - 488
195ASNASNLEULEULJ10 - 4909 - 489
295ASNASNLEULEUlBA10 - 4909 - 489
196ASNASNGLNGLNLJ10 - 4899 - 488
296ASNASNGLNGLNrFA10 - 4899 - 488
197ASNASNLEULEULJ10 - 4909 - 489
297ASNASNLEULEUtHA10 - 4909 - 489
198DGDGDTDTNK1 - 20201 - 20
298DGDGDTDTOL1 - 201 - 20
199DGDGDCDCNK1 - 20181 - 18
299DGDGDCDCVQ1 - 20181 - 18
1100DGDGDTDTNK1 - 20201 - 20
2100DGDGDTDTWR1 - 20201 - 20
1101DGDGDTDTNK1 - 20201 - 20
2101DGDGDTDTeW1 - 201 - 20
1102DGDGDCDCNK3 - 20183 - 18
2102DGDGDCDCfX3 - 181 - 16
1103DGDGDTDTNK1 - 20201 - 20
2103DGDGDTDTnCA1 - 20201 - 20
1104DADADCDCNK2 - 20182 - 18
2104DADADCDCoDA2 - 20182 - 18
1105DADADTDTNK2 - 20192 - 19
2105DADADTDTvIA2 - 20192 - 19
1106DGDGDTDTNK1 - 20201 - 20
2106DGDGDTDTwJA1 - 20201 - 20
1107DGDGDCDCOL1 - 181 - 18
2107DGDGDCDCVQ1 - 20181 - 18
1108DGDGDTDTOL1 - 201 - 20
2108DGDGDTDTWR1 - 20201 - 20
1109DGDGDTDTOL1 - 201 - 20
2109DGDGDTDTeW1 - 201 - 20
1110DGDGDCDCOL3 - 183 - 18
2110DGDGDCDCfX3 - 181 - 16
1111DGDGDTDTOL1 - 201 - 20
2111DGDGDTDTnCA1 - 20201 - 20
1112DADADCDCOL2 - 182 - 18
2112DADADCDCoDA2 - 20182 - 18
1113DADADTDTOL2 - 192 - 19
2113DADADTDTvIA2 - 20192 - 19
1114DGDGDTDTOL1 - 201 - 20
2114DGDGDTDTwJA1 - 20201 - 20
1115LYSLYSVALVALSM417 - 6382 - 186
2115LYSLYSVALVALUO417 - 6381 - 188
1116LYSLYSVALVALSM417 - 6382 - 186
2116LYSLYSVALVALbS417 - 6382 - 186
1117LYSLYSALAALASM417 - 6372 - 185
2117LYSLYSALAALAdU417 - 6371 - 181
1118LYSLYSALAALASM417 - 6372 - 185
2118LYSLYSALAALAkY417 - 6372 - 185
1119LYSLYSVALVALSM417 - 6382 - 186
2119LYSLYSVALVALmAA417 - 6381 - 188
1120LYSLYSALAALASM417 - 6372 - 185
2120LYSLYSALAALAsEA417 - 6372 - 185
1121LYSLYSALAALASM417 - 6372 - 185
2121LYSLYSALAALAuGA417 - 6371 - 187
1122ASNASNGLNGLNRN10 - 4899 - 488
2122ASNASNGLNGLNTP10 - 4899 - 488
1123GLUGLULEULEURN11 - 49010 - 489
2123GLUGLULEULEUaT11 - 49010 - 489
1124ASNASNGLNGLNRN10 - 4899 - 488
2124ASNASNGLNGLNcV10 - 4899 - 488
1125ASNASNGLYGLYRN10 - 4919 - 490
2125ASNASNGLYGLYjZ10 - 4919 - 490
1126ASNASNGLNGLNRN10 - 4899 - 488
2126ASNASNGLNGLNlBA10 - 4899 - 488
1127ASNASNLEULEURN10 - 4909 - 489
2127ASNASNLEULEUrFA10 - 4909 - 489
1128ASNASNGLNGLNRN10 - 4899 - 488
2128ASNASNGLNGLNtHA10 - 4899 - 488
1129LYSLYSVALVALUO417 - 6381 - 188
2129LYSLYSVALVALbS417 - 6382 - 186
1130LYSLYSALAALAUO417 - 6371 - 187
2130LYSLYSALAALAdU417 - 6371 - 181
1131LYSLYSVALVALUO417 - 6381 - 188
2131LYSLYSVALVALkY417 - 6382 - 186
1132LYSLYSVALVALUO417 - 6381 - 188
2132LYSLYSVALVALmAA417 - 6381 - 188
1133LYSLYSVALVALUO417 - 6381 - 188
2133LYSLYSVALVALsEA417 - 6382 - 186
1134LYSLYSASNASNUO417 - 6361 - 186
2134LYSLYSASNASNuGA417 - 6361 - 186
1135GLUGLUGLNGLNTP11 - 48910 - 488
2135GLUGLUGLNGLNaT11 - 48910 - 488
1136ASNASNGLNGLNTP10 - 4899 - 488
2136ASNASNGLNGLNcV10 - 4899 - 488
1137ASNASNGLNGLNTP10 - 4899 - 488
2137ASNASNGLNGLNjZ10 - 4899 - 488
1138ASNASNLEULEUTP10 - 4909 - 489
2138ASNASNLEULEUlBA10 - 4909 - 489
1139ASNASNGLNGLNTP10 - 4899 - 488
2139ASNASNGLNGLNrFA10 - 4899 - 488
1140ASNASNLEULEUTP10 - 4909 - 489
2140ASNASNLEULEUtHA10 - 4909 - 489
1141DGDGDCDCVQ1 - 20181 - 18
2141DGDGDCDCWR1 - 20181 - 18
1142DGDGDCDCVQ1 - 20181 - 18
2142DGDGDCDCeW1 - 181 - 18
1143DGDGDCDCVQ3 - 20183 - 18
2143DGDGDCDCfX3 - 181 - 16
1144DGDGDCDCVQ1 - 20181 - 18
2144DGDGDCDCnCA1 - 20181 - 18
1145DADADCDCVQ2 - 20182 - 18
2145DADADCDCoDA2 - 20182 - 18
1146DADADCDCVQ2 - 20182 - 18
2146DADADCDCvIA2 - 20182 - 18
1147DGDGDCDCVQ1 - 20181 - 18
2147DGDGDCDCwJA1 - 20181 - 18
1148DGDGDTDTWR1 - 20201 - 20
2148DGDGDTDTeW1 - 201 - 20
1149DGDGDCDCWR3 - 20183 - 18
2149DGDGDCDCfX3 - 181 - 16
1150DGDGDTDTWR1 - 20201 - 20
2150DGDGDTDTnCA1 - 20201 - 20
1151DADADCDCWR2 - 20182 - 18
2151DADADCDCoDA2 - 20182 - 18
1152DADADTDTWR2 - 20192 - 19
2152DADADTDTvIA2 - 20192 - 19
1153DGDGDTDTWR1 - 20201 - 20
2153DGDGDTDTwJA1 - 20201 - 20
1154LYSLYSALAALAbS417 - 6372 - 185
2154LYSLYSALAALAdU417 - 6371 - 181
1155LYSLYSALAALAbS417 - 6372 - 185
2155LYSLYSALAALAkY417 - 6372 - 185
1156LYSLYSVALVALbS417 - 6382 - 186
2156LYSLYSVALVALmAA417 - 6381 - 188
1157LYSLYSALAALAbS417 - 6372 - 185
2157LYSLYSALAALAsEA417 - 6372 - 185
1158LYSLYSALAALAbS417 - 6372 - 185
2158LYSLYSALAALAuGA417 - 6371 - 187
1159GLUGLUGLNGLNaT11 - 48910 - 488
2159GLUGLUGLNGLNcV11 - 48910 - 488
1160GLUGLULEULEUaT11 - 49010 - 489
2160GLUGLULEULEUjZ11 - 49010 - 489
1161GLUGLUGLNGLNaT11 - 48910 - 488
2161GLUGLUGLNGLNlBA11 - 48910 - 488
1162GLUGLULEULEUaT11 - 49010 - 489
2162GLUGLULEULEUrFA11 - 49010 - 489
1163GLUGLUGLNGLNaT11 - 48910 - 488
2163GLUGLUGLNGLNtHA11 - 48910 - 488
1164LYSLYSASNASNdU417 - 6361 - 180
2164LYSLYSASNASNkY417 - 6362 - 184
1165LYSLYSALAALAdU417 - 6371 - 181
2165LYSLYSALAALAmAA417 - 6371 - 187
1166LYSLYSALAALAdU417 - 6371 - 181
2166LYSLYSALAALAsEA417 - 6372 - 185
1167LYSLYSALAALAdU417 - 6371 - 181
2167LYSLYSALAALAuGA417 - 6371 - 187
1168ASNASNGLNGLNcV10 - 4899 - 488
2168ASNASNGLNGLNjZ10 - 4899 - 488
1169ASNASNGLNGLNcV10 - 4899 - 488
2169ASNASNGLNGLNlBA10 - 4899 - 488
1170ILEILEGLNGLNcV9 - 4898 - 488
2170ILEILEGLNGLNrFA9 - 4898 - 488
1171ASNASNGLNGLNcV10 - 4899 - 488
2171ASNASNGLNGLNtHA10 - 4899 - 488
1172DGDGDCDCeW3 - 183 - 18
2172DGDGDCDCfX3 - 181 - 16
1173DGDGDTDTeW1 - 201 - 20
2173DGDGDTDTnCA1 - 20201 - 20
1174DADADCDCeW2 - 182 - 18
2174DADADCDCoDA2 - 20182 - 18
1175DADADTDTeW2 - 192 - 19
2175DADADTDTvIA2 - 20192 - 19
1176DGDGDTDTeW1 - 201 - 20
2176DGDGDTDTwJA1 - 20201 - 20
1177DGDGDCDCfX3 - 181 - 16
2177DGDGDCDCnCA3 - 20183 - 18
1178DGDGDCDCfX3 - 181 - 16
2178DGDGDCDCoDA3 - 20183 - 18
1179DGDGDCDCfX3 - 181 - 16
2179DGDGDCDCvIA3 - 20183 - 18
1180DGDGDCDCfX3 - 181 - 16
2180DGDGDCDCwJA3 - 20183 - 18
1181LYSLYSVALVALkY417 - 6382 - 186
2181LYSLYSVALVALmAA417 - 6381 - 188
1182GLYGLYALAALAkY416 - 6371 - 185
2182GLYGLYALAALAsEA416 - 6371 - 185
1183LYSLYSASNASNkY417 - 6362 - 184
2183LYSLYSASNASNuGA417 - 6361 - 186
1184ASNASNGLNGLNjZ10 - 4899 - 488
2184ASNASNGLNGLNlBA10 - 4899 - 488
1185ASNASNLEULEUjZ10 - 4909 - 489
2185ASNASNLEULEUrFA10 - 4909 - 489
1186ASNASNGLNGLNjZ10 - 4899 - 488
2186ASNASNGLNGLNtHA10 - 4899 - 488
1187LYSLYSVALVALmAA417 - 6381 - 188
2187LYSLYSVALVALsEA417 - 6382 - 186
1188LYSLYSASNASNmAA417 - 6361 - 186
2188LYSLYSASNASNuGA417 - 6361 - 186
1189ASNASNGLNGLNlBA10 - 4899 - 488
2189ASNASNGLNGLNrFA10 - 4899 - 488
1190ASNASNLEULEUlBA10 - 4909 - 489
2190ASNASNLEULEUtHA10 - 4909 - 489
1191DADADCDCnCA2 - 20182 - 18
2191DADADCDCoDA2 - 20182 - 18
1192DADADTDTnCA2 - 20192 - 19
2192DADADTDTvIA2 - 20192 - 19
1193DGDGDTDTnCA1 - 20201 - 20
2193DGDGDTDTwJA1 - 20201 - 20
1194DADADCDCoDA2 - 20182 - 18
2194DADADCDCvIA2 - 20182 - 18
1195DADADCDCoDA2 - 20182 - 18
2195DADADCDCwJA2 - 20182 - 18
1196LYSLYSALAALAsEA417 - 6372 - 185
2196LYSLYSALAALAuGA417 - 6371 - 187
1197ASNASNGLNGLNrFA10 - 4899 - 488
2197ASNASNGLNGLNtHA10 - 4899 - 488
1198DADADTDTvIA2 - 20192 - 19
2198DADADTDTwJA2 - 20192 - 19

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
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198

-
Components

-
DNA gyrase subunit ... , 9 types, 24 molecules BSbsACLRTacjlrtDUmKJMdku

#1: Protein
DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 20846.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, gyrB, SAV0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0K8, UniProt: P66936, EC: 5.99.1.3
#2: Protein
DNA gyrase subunit A /


Mass: 55537.312 Da / Num. of mol.: 11 / Mutation: 123 phosphotyrosine
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3
#3: Protein DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 21111.018 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, gyrB, SAR0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0K8, UniProt: Q6GKU0, EC: 5.99.1.3
#5: Protein DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 21009.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005, gyrB, SAUSA300_0005 / Production host: Escherichia coli (E. coli)
References: UniProt: P66937, UniProt: Q2FKQ1, UniProt: P0A0K8*PLUS, EC: 5.99.1.3
#6: Protein DNA gyrase subunit A /


Mass: 54370.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3
#7: Protein DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 21274.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005, gyrB, SAUSA300_0005 / Production host: Escherichia coli (E. coli)
References: UniProt: P66937, UniProt: Q2FKQ1, UniProt: P0A0K8*PLUS, EC: 5.99.1.3
#9: Protein DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 20363.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005, gyrB, SAR0005 / Production host: Escherichia coli (E. coli)
References: UniProt: P66937, UniProt: Q6GKU0, UniProt: P0A0K8*PLUS, EC: 5.99.1.3
#11: Protein DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 21080.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005, gyrB, SAR0005 / Production host: Escherichia coli (E. coli)
References: UniProt: P66937, UniProt: Q6GKU0, UniProt: P0A0K8*PLUS, EC: 5.99.1.3
#12: Protein DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 21011.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005, gyrB, SAUSA300_0005 / Production host: Escherichia coli (E. coli)
References: UniProt: P66937, UniProt: Q2FKQ1, UniProt: P0A0K8*PLUS, EC: 5.99.1.3

-
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)- ... , 3 types, 12 molecules EFNOWenvwVof

#4: DNA chain
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')


Mass: 6150.966 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#8: DNA chain DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')


Mass: 5846.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#10: DNA chain DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')


Mass: 5204.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

-
Non-polymers , 1 types, 12 molecules

#13: Chemical
ChemComp-JK8 / (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine


Mass: 364.825 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H17ClN2O2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 10% perg 5k mme, 150mM Bis Tris pH6.2 - see paper for details.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.525
11-H-4/2L, -K, L20.475
ReflectionResolution: 3.4→162.15 Å / Num. obs: 135780 / % possible obs: 81.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.077 / Rrim(I) all: 0.144 / Net I/σ(I): 10.6
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.369 / Num. unique obs: 20498 / Rpim(I) all: 0.237 / Rrim(I) all: 0.44 / % possible all: 83.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XCS
Resolution: 3.4→162.15 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.879 / SU B: 20.499 / SU ML: 0.343 / Cross valid method: THROUGHOUT / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20834 6786 5 %RANDOM
Rwork0.17627 ---
obs0.17787 128993 80.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.745 Å2
Baniso -1Baniso -2Baniso -3
1-7.76 Å20 Å2-1.93 Å2
2--15.83 Å20 Å2
3----23.59 Å2
Refinement stepCycle: LAST / Resolution: 3.4→162.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61755 4642 312 0 66709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01369826
X-RAY DIFFRACTIONr_bond_other_d0.0030.01762645
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.61195659
X-RAY DIFFRACTIONr_angle_other_deg1.2371.642144583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14758294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.38221.4513735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.821511236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.57415652
X-RAY DIFFRACTIONr_chiral_restr0.0580.29378
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0277551
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0215141
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_it5.1955.76632804
X-RAY DIFFRACTIONr_mcbond_other5.1955.76632803
X-RAY DIFFRACTIONr_mcangle_it8.438.6441197
X-RAY DIFFRACTIONr_mcangle_other8.438.6441198
X-RAY DIFFRACTIONr_scbond_it4.9446.02537022
X-RAY DIFFRACTIONr_scbond_other4.9446.02537023
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0698.9454454
X-RAY DIFFRACTIONr_long_range_B_refined15.951284993
X-RAY DIFFRACTIONr_long_range_B_other15.951284994
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)
11B55760.08
12D55760.08
21B57630.04
22K57630.04
31B55670.08
32M55670.08
41B57880.04
42S57880.04
51B55850.08
52U55850.08
61B57660.03
62b57660.03
71B54080.08
72d54080.08
81B57560.02
82k57560.02
91B55590.08
92m55590.08
101B57700.02
102s57700.02
111B55550.08
112u55550.08
121A154450.07
122C154450.07
131A158290.05
132J158290.05
141A154440.07
142L154440.07
151A157440.06
152R157440.06
161A154630.07
162T154630.07
171A157830.05
172a157830.05
181A154820.07
182c154820.07
191A158050.05
192j158050.05
201A154860.07
202l154860.07
211A158180.05
212r158180.05
221A154920.07
222t154920.07
231D54990.08
232K54990.08
241D58560.04
242M58560.04
251D54570.08
252S54570.08
261D58970.04
262U58970.04
271D54360.08
272b54360.08
281D56470.03
282d56470.03
291D54610.08
292k54610.08
301D58570.04
302m58570.04
311D54690.08
312s54690.08
321D58420.04
322u58420.04
331C154050.06
332J154050.06
341C158100.03
342L158100.03
351C154020.06
352R154020.06
361C158000.03
362T158000.03
371C154530.06
372a154530.06
381C158820.03
382c158820.03
391C154220.06
392j154220.06
401C158590.02
402l158590.02
411C154580.06
412r154580.06
421C158650.03
422t158650.03
431E13230.07
432F13230.07
441E13380.07
442N13380.07
451E13300.07
452O13300.07
461E12380.05
462V12380.05
471E13260.1
472W13260.1
481E13070.08
482e13070.08
491E12430.06
492f12430.06
501E13090.1
502n13090.1
511E12220.07
512o12220.07
521E13210.05
522v13210.05
531E13140.08
532w13140.08
541F14890.09
542N14890.09
551F15250.07
552O15250.07
561F13770.1
562V13770.1
571F14780.09
572W14780.09
581F14250.12
582e14250.12
591F12390.07
592f12390.07
601F14710.1
602n14710.1
611F13210.07
612o13210.07
621F14070.07
622v14070.07
631F14970.08
632w14970.08
641K55830.08
642M55830.08
651K57210.05
652S57210.05
661K55810.08
662U55810.08
671K56990.04
672b56990.04
681K54130.08
682d54130.08
691K57490.05
692k57490.05
701K55650.08
702m55650.08
711K57500.04
712s57500.04
721K55650.08
722u55650.08
731J156160.06
732L156160.06
741J160030.04
742R160030.04
751J155990.07
752T155990.07
761J160070.03
762a160070.03
771J156490.07
772c156490.07
781J160540.04
782j160540.04
791J156680.06
792l156680.06
801J160200.04
802r160200.04
811J156470.06
812t156470.06
821M54720.09
822S54720.09
831M59130.04
832U59130.04
841M54590.08
842b54590.08
851M56630.04
852d56630.04
861M55050.09
862k55050.09
871M58780.03
872m58780.03
881M54790.08
882s54790.08
891M58820.04
892u58820.04
901L153330.07
902R153330.07
911L157480.04
912T157480.04
921L153420.06
922a153420.06
931L157770.04
932c157770.04
941L153300.07
942j153300.07
951L157700.04
952l157700.04
961L154290.06
962r154290.06
971L158040.04
972t158040.04
981N13430.07
982O13430.07
991N12360.07
992V12360.07
1001N13280.09
1002W13280.09
1011N13170.09
1012e13170.09
1021N12400.06
1022f12400.06
1031N13390.1
1032n13390.1
1041N12280.06
1042o12280.06
1051N13230.06
1052v13230.06
1061N13100.07
1062w13100.07
1071O13780.1
1072V13780.1
1081O14800.08
1082W14800.08
1091O14340.11
1092e14340.11
1101O12420.06
1102f12420.06
1111O14870.09
1112n14870.09
1121O13350.06
1122o13350.06
1131O14070.07
1132v14070.07
1141O14970.08
1142w14970.08
1151S55870.08
1152U55870.08
1161S57840.04
1162b57840.04
1171S54240.08
1172d54240.08
1181S57670.03
1182k57670.03
1191S55770.08
1192m55770.08
1201S57840.03
1202s57840.03
1211S55710.08
1212u55710.08
1221R155170.07
1222T155170.07
1231R158950.04
1232a158950.04
1241R155540.07
1242c155540.07
1251R159120.05
1252j159120.05
1261R156040.06
1262l156040.06
1271R159110.05
1272r159110.05
1281R155370.07
1282t155370.07
1291U54720.08
1292b54720.08
1301U56830.03
1302d56830.03
1311U54920.08
1312k54920.08
1321U59320.03
1322m59320.03
1331U54970.08
1332s54970.08
1341U59250.03
1342u59250.03
1351T153470.06
1352a153470.06
1361T158070.04
1362c158070.04
1371T153630.07
1372j153630.07
1381T158100.04
1382l158100.04
1391T153970.07
1392r153970.07
1401T158730.03
1402t158730.03
1411V13750.1
1412W13750.1
1421V13340.09
1422e13340.09
1431V12250.06
1432f12250.06
1441V13660.1
1442n13660.1
1451V13040.08
1452o13040.08
1461V13190.08
1462v13190.08
1471V13680.1
1472w13680.1
1481W14250.12
1482e14250.12
1491W12250.06
1492f12250.06
1501W14690.1
1502n14690.1
1511W13220.06
1512o13220.06
1521W14040.08
1522v14040.08
1531W14860.11
1532w14860.11
1541b54060.08
1542d54060.08
1551b57140.03
1552k57140.03
1561b55520.08
1562m55520.08
1571b57300.02
1572s57300.02
1581b55420.07
1582u55420.07
1591a155460.06
1592c155460.06
1601a159170.04
1602j159170.04
1611a155590.06
1612l155590.06
1621a159270.04
1622r159270.04
1631a155360.06
1632t155360.06
1641d52840.08
1642k52840.08
1651d56400.03
1652m56400.03
1661d53100.08
1662s53100.08
1671d56500.03
1672u56500.03
1681c153920.07
1682j153920.07
1691c158270.03
1692l158270.03
1701c154390.07
1702r154390.07
1711c158520.03
1712t158520.03
1721e12110.07
1722f12110.07
1731e14140.12
1732n14140.12
1741e13040.09
1742o13040.09
1751e13680.1
1752v13680.1
1761e14070.11
1762w14070.11
1771f12140.08
1772n12140.08
1781f12190.07
1782o12190.07
1791f12250.05
1792v12250.05
1801f12210.07
1802w12210.07
1811k55380.08
1812m55380.08
1821k57550.03
1822s57550.03
1831k55120.08
1832u55120.08
1841j156240.06
1842l156240.06
1851j159670.05
1852r159670.05
1861j155900.06
1862t155900.06
1871m54240.08
1872s54240.08
1881m58300.03
1882u58300.03
1891l153760.07
1892r153760.07
1901l157940.03
1902t157940.03
1911n13210.08
1912o13210.08
1921n13910.09
1922v13910.09
1931n14420.1
1932w14420.1
1941o13100.08
1942v13100.08
1951o13130.08
1952w13130.08
1961s55310.08
1962u55310.08
1971r156960.07
1972t156960.07
1981v13940.08
1982w13940.08
LS refinement shellResolution: 3.39→3.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 451 -
Rwork0.209 8831 -
obs--74.07 %

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