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- PDB-4z88: SH3-II of Drosophila Rim-binding protein with Aplip1 peptide -

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Basic information

Entry
Database: PDB / ID: 4z88
TitleSH3-II of Drosophila Rim-binding protein with Aplip1 peptide
Components
  • JNK-interacting protein 1
  • RIM-binding protein, isoform F
KeywordsRIM-BINDING PROTEIN / Synapse / Active Zone / SH3 domain / Aplip1
Function / homology
Function and homology information


retrograde synaptic vesicle transport / presynaptic active zone organization / Pregnenolone biosynthesis / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / cytoskeletal matrix organization at active zone / cytoskeleton of presynaptic active zone ...retrograde synaptic vesicle transport / presynaptic active zone organization / Pregnenolone biosynthesis / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / cytoskeletal matrix organization at active zone / cytoskeleton of presynaptic active zone / anterograde synaptic vesicle transport / regulation of terminal button organization / neuromuscular synaptic transmission / presynaptic active zone cytoplasmic component / MAP-kinase scaffold activity / axonal transport of mitochondrion / kinesin binding / regulation of JNK cascade / JNK cascade / axon cytoplasm / neuromuscular junction / axon / protein kinase binding / identical protein binding / metal ion binding
Similarity search - Function
RIMS-binding protein, second SH3 domain / RIMS-binding protein, third SH3 domain / RIMS-binding protein 1/2/3 / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Variant SH3 domain ...RIMS-binding protein, second SH3 domain / RIMS-binding protein, third SH3 domain / RIMS-binding protein 1/2/3 / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Variant SH3 domain / SH3 Domains / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / RIM-binding protein, isoform F / JNK-interacting protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsDriller, J.H. / Holton, N. / Siebert, M. / Boehme, M.A. / Wahl, M.C. / Sigrist, S.J. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB958 Germany
CitationJournal: Elife / Year: 2015
Title: A high affinity RIM-binding protein/Aplip1 interaction prevents the formation of ectopic axonal active zones.
Authors: Siebert, M. / Bohme, M.A. / Driller, J.H. / Babikir, H. / Mampell, M.M. / Rey, U. / Ramesh, N. / Matkovic, T. / Holton, N. / Reddy-Alla, S. / Gottfert, F. / Kamin, D. / Quentin, C. / ...Authors: Siebert, M. / Bohme, M.A. / Driller, J.H. / Babikir, H. / Mampell, M.M. / Rey, U. / Ramesh, N. / Matkovic, T. / Holton, N. / Reddy-Alla, S. / Gottfert, F. / Kamin, D. / Quentin, C. / Klinedinst, S. / Andlauer, T.F. / Hell, S.W. / Collins, C.A. / Wahl, M.C. / Loll, B. / Sigrist, S.J.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / 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 / _pdbx_audit_support.funding_organization / _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
A: RIM-binding protein, isoform F
B: RIM-binding protein, isoform F
C: RIM-binding protein, isoform F
D: RIM-binding protein, isoform F
E: RIM-binding protein, isoform F
F: RIM-binding protein, isoform F
G: RIM-binding protein, isoform F
H: RIM-binding protein, isoform F
I: RIM-binding protein, isoform F
J: RIM-binding protein, isoform F
K: RIM-binding protein, isoform F
L: RIM-binding protein, isoform F
M: JNK-interacting protein 1
N: JNK-interacting protein 1
O: JNK-interacting protein 1
P: JNK-interacting protein 1
Q: JNK-interacting protein 1
R: JNK-interacting protein 1
S: JNK-interacting protein 1
T: JNK-interacting protein 1
U: JNK-interacting protein 1
V: JNK-interacting protein 1
W: JNK-interacting protein 1
X: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,79835
Polymers122,75324
Non-polymers1,04511
Water1,02757
1
A: RIM-binding protein, isoform F
M: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIM-binding protein, isoform F
N: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RIM-binding protein, isoform F
O: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RIM-binding protein, isoform F
P: JNK-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)10,2292
Polymers10,2292
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RIM-binding protein, isoform F
Q: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: RIM-binding protein, isoform F
R: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: RIM-binding protein, isoform F
S: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: RIM-binding protein, isoform F
T: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: RIM-binding protein, isoform F
U: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: RIM-binding protein, isoform F
V: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: RIM-binding protein, isoform F
W: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: RIM-binding protein, isoform F
X: JNK-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3243
Polymers10,2292
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.280, 62.420, 163.640
Angle α, β, γ (deg.)90.00, 90.27, 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
27H
18A
28I
19A
29J
110A
210K
111A
211L
112B
212C
113B
213D
114B
214E
115B
215F
116B
216G
117B
217H
118B
218I
119B
219J
120B
220K
121B
221L
122C
222D
123C
223E
124C
224F
125C
225G
126C
226H
127C
227I
128C
228J
129C
229K
130C
230L
131D
231E
132D
232F
133D
233G
134D
234H
135D
235I
136D
236J
137D
237K
138D
238L
139E
239F
140E
240G
141E
241H
142E
242I
143E
243J
144E
244K
145E
245L
146F
246G
147F
247H
148F
248I
149F
249J
150F
250K
151F
251L
152G
252H
153G
253I
154G
254J
155G
255K
156G
256L
157H
257I
158H
258J
159H
259K
160H
260L
161I
261J
162I
262K
163I
263L
164J
264K
165J
265L
166K
266L
167M
267Q
168M
268S
169M
269U
170M
270W
171Q
271S
172Q
272U
173Q
273W
174S
274U
175S
275W
176U
276W

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGVALVALAA1318 - 13819 - 72
21ARGARGVALVALBB1318 - 13819 - 72
12ARGARGGLUGLUAA1318 - 13809 - 71
22ARGARGGLUGLUCC1318 - 13809 - 71
13ARGARGVALVALAA1318 - 13819 - 72
23ARGARGVALVALDD1318 - 13819 - 72
14TYRTYRGLUGLUAA1319 - 138010 - 71
24TYRTYRGLUGLUEE1319 - 138010 - 71
15ARGARGSERSERAA1318 - 13799 - 70
25ARGARGSERSERFF1318 - 13799 - 70
16ARGARGGLUGLUAA1318 - 13809 - 71
26ARGARGGLUGLUGG1318 - 13809 - 71
17ARGARGVALVALAA1318 - 13819 - 72
27ARGARGVALVALHH1318 - 13819 - 72
18ARGARGVALVALAA1318 - 13819 - 72
28ARGARGVALVALII1318 - 13819 - 72
19ARGARGGLUGLUAA1318 - 13809 - 71
29ARGARGGLUGLUJJ1318 - 13809 - 71
110ARGARGGLUGLUAA1318 - 13809 - 71
210ARGARGGLUGLUKK1318 - 13809 - 71
111ARGARGGLUGLUAA1318 - 13809 - 71
211ARGARGGLUGLULL1318 - 13809 - 71
112PHEPHEGLUGLUBB1317 - 13808 - 71
212PHEPHEGLUGLUCC1317 - 13808 - 71
113PHEPHEVALVALBB1317 - 13818 - 72
213PHEPHEVALVALDD1317 - 13818 - 72
114TYRTYRGLUGLUBB1319 - 138010 - 71
214TYRTYRGLUGLUEE1319 - 138010 - 71
115PHEPHESERSERBB1317 - 13798 - 70
215PHEPHESERSERFF1317 - 13798 - 70
116PHEPHEGLUGLUBB1317 - 13808 - 71
216PHEPHEGLUGLUGG1317 - 13808 - 71
117PHEPHEVALVALBB1317 - 13818 - 72
217PHEPHEVALVALHH1317 - 13818 - 72
118PHEPHEGLUGLUBB1317 - 13828 - 73
218PHEPHEGLUGLUII1317 - 13828 - 73
119PHEPHEGLUGLUBB1317 - 13808 - 71
219PHEPHEGLUGLUJJ1317 - 13808 - 71
120PHEPHEGLUGLUBB1317 - 13808 - 71
220PHEPHEGLUGLUKK1317 - 13808 - 71
121PHEPHEGLUGLUBB1317 - 13808 - 71
221PHEPHEGLUGLULL1317 - 13808 - 71
122PHEPHEGLUGLUCC1317 - 13808 - 71
222PHEPHEGLUGLUDD1317 - 13808 - 71
123TYRTYRGLUGLUCC1319 - 138010 - 71
223TYRTYRGLUGLUEE1319 - 138010 - 71
124PHEPHESERSERCC1317 - 13798 - 70
224PHEPHESERSERFF1317 - 13798 - 70
125PHEPHEGLUGLUCC1317 - 13808 - 71
225PHEPHEGLUGLUGG1317 - 13808 - 71
126PHEPHEGLUGLUCC1317 - 13808 - 71
226PHEPHEGLUGLUHH1317 - 13808 - 71
127PHEPHEGLUGLUCC1317 - 13808 - 71
227PHEPHEGLUGLUII1317 - 13808 - 71
128PHEPHEGLUGLUCC1317 - 13808 - 71
228PHEPHEGLUGLUJJ1317 - 13808 - 71
129PHEPHEGLUGLUCC1317 - 13808 - 71
229PHEPHEGLUGLUKK1317 - 13808 - 71
130PHEPHEGLUGLUCC1317 - 13808 - 71
230PHEPHEGLUGLULL1317 - 13808 - 71
131TYRTYRGLUGLUDD1319 - 138010 - 71
231TYRTYRGLUGLUEE1319 - 138010 - 71
132SERSERSERSERDD1314 - 13795 - 70
232SERSERSERSERFF1314 - 13795 - 70
133PROPROGLUGLUDD1315 - 13806 - 71
233PROPROGLUGLUGG1315 - 13806 - 71
134GLYGLYGLUGLUDD1313 - 13824 - 73
234GLYGLYGLUGLUHH1313 - 13824 - 73
135PHEPHEVALVALDD1317 - 13818 - 72
235PHEPHEVALVALII1317 - 13818 - 72
136SERSERGLUGLUDD1314 - 13805 - 71
236SERSERGLUGLUJJ1314 - 13805 - 71
137GLUGLUGLUGLUDD1316 - 13807 - 71
237GLUGLUGLUGLUKK1316 - 13807 - 71
138SERSERGLUGLUDD1314 - 13805 - 71
238SERSERGLUGLULL1314 - 13805 - 71
139TYRTYRSERSEREE1319 - 137910 - 70
239TYRTYRSERSERFF1319 - 137910 - 70
140TYRTYRGLUGLUEE1319 - 138010 - 71
240TYRTYRGLUGLUGG1319 - 138010 - 71
141TYRTYRGLUGLUEE1319 - 138010 - 71
241TYRTYRGLUGLUHH1319 - 138010 - 71
142TYRTYRGLUGLUEE1319 - 138010 - 71
242TYRTYRGLUGLUII1319 - 138010 - 71
143TYRTYRGLUGLUEE1319 - 138010 - 71
243TYRTYRGLUGLUJJ1319 - 138010 - 71
144TYRTYRGLUGLUEE1319 - 138010 - 71
244TYRTYRGLUGLUKK1319 - 138010 - 71
145TYRTYRGLUGLUEE1319 - 138010 - 71
245TYRTYRGLUGLULL1319 - 138010 - 71
146PROPROSERSERFF1315 - 13796 - 70
246PROPROSERSERGG1315 - 13796 - 70
147SERSERSERSERFF1314 - 13795 - 70
247SERSERSERSERHH1314 - 13795 - 70
148PHEPHESERSERFF1317 - 13798 - 70
248PHEPHESERSERII1317 - 13798 - 70
149SERSERSERSERFF1314 - 13795 - 70
249SERSERSERSERJJ1314 - 13795 - 70
150GLUGLUSERSERFF1316 - 13797 - 70
250GLUGLUSERSERKK1316 - 13797 - 70
151SERSERSERSERFF1314 - 13795 - 70
251SERSERSERSERLL1314 - 13795 - 70
152PROPROGLUGLUGG1315 - 13806 - 71
252PROPROGLUGLUHH1315 - 13806 - 71
153PHEPHEGLUGLUGG1317 - 13808 - 71
253PHEPHEGLUGLUII1317 - 13808 - 71
154PROPROGLUGLUGG1315 - 13806 - 71
254PROPROGLUGLUJJ1315 - 13806 - 71
155GLUGLUGLUGLUGG1316 - 13807 - 71
255GLUGLUGLUGLUKK1316 - 13807 - 71
156PROPROGLUGLUGG1315 - 13806 - 71
256PROPROGLUGLULL1315 - 13806 - 71
157PHEPHEVALVALHH1317 - 13818 - 72
257PHEPHEVALVALII1317 - 13818 - 72
158SERSERGLUGLUHH1314 - 13805 - 71
258SERSERGLUGLUJJ1314 - 13805 - 71
159GLUGLUGLUGLUHH1316 - 13807 - 71
259GLUGLUGLUGLUKK1316 - 13807 - 71
160SERSERGLUGLUHH1314 - 13805 - 71
260SERSERGLUGLULL1314 - 13805 - 71
161PHEPHEGLUGLUII1317 - 13808 - 71
261PHEPHEGLUGLUJJ1317 - 13808 - 71
162PHEPHEGLUGLUII1317 - 13808 - 71
262PHEPHEGLUGLUKK1317 - 13808 - 71
163PHEPHEGLUGLUII1317 - 13808 - 71
263PHEPHEGLUGLULL1317 - 13808 - 71
164GLUGLUGLUGLUJJ1316 - 13807 - 71
264GLUGLUGLUGLUKK1316 - 13807 - 71
165SERSERVALVALJJ1314 - 13815 - 72
265SERSERVALVALLL1314 - 13815 - 72
166GLUGLUGLUGLUKK1316 - 13807 - 71
266GLUGLUGLUGLULL1316 - 13807 - 71
167ARGARGLYSLYSMM153 - 1636 - 16
267ARGARGLYSLYSQQ153 - 1636 - 16
168ARGARGLYSLYSMM153 - 1636 - 16
268ARGARGLYSLYSSS153 - 1636 - 16
169ARGARGLYSLYSMM153 - 1636 - 16
269ARGARGLYSLYSUU153 - 1636 - 16
170ARGARGLYSLYSMM153 - 1636 - 16
270ARGARGLYSLYSWW153 - 1636 - 16
171ARGARGNH2NH2QQ151 - 1644 - 17
271ARGARGNH2NH2SS151 - 1644 - 17
172ARGARGLYSLYSQQ152 - 1635 - 16
272ARGARGLYSLYSUU152 - 1635 - 16
173ARGARGLYSLYSQQ152 - 1635 - 16
273ARGARGLYSLYSWW152 - 1635 - 16
174ARGARGLYSLYSSS152 - 1635 - 16
274ARGARGLYSLYSUU152 - 1635 - 16
175ARGARGLYSLYSSS152 - 1635 - 16
275ARGARGLYSLYSWW152 - 1635 - 16
176ARGARGNH2NH2UU152 - 1645 - 17
276ARGARGNH2NH2WW152 - 1645 - 17

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

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Components

#1: Protein
RIM-binding protein, isoform F


Mass: 8277.036 Da / Num. of mol.: 12 / Fragment: UNP residues 1318-1382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Rbp, Dmel_CG43073 / Plasmid: pGex6p1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4JDC9
#2: Protein/peptide
JNK-interacting protein 1 / JIP-1 / APP-like-interacting protein 1 / APLIP1 / Protein eye developmental SP512


Mass: 1952.421 Da / Num. of mol.: 12 / Fragment: UNP residues 149-163 / Source method: obtained synthetically / Details: N-terminal acetylation, C-terminal amidation / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W0K0
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 100 mM Bicine, 2.2-2.6 M Ammoniumsulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 19, 2013
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.135
11-1/2H-3/2K, -1/2H+1/2K, -L20.126
11-1/2H+3/2K, 1/2H+1/2K, -L30.146
111/2H-3/2K, -1/2H-1/2K, -L40.193
111/2H+3/2K, 1/2H-1/2K, -L50.182
11-h,-k,l60.218
ReflectionResolution: 2.09→50 Å / Num. obs: 64269 / % possible obs: 98.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 2.09→2.19 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.6 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CSQ
Resolution: 2.09→45.25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.475 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23642 3011 4.7 %Rfree reflections was generated in P622 and then expanded to C2 to insure equal distribution of the Rfree reflections in all six twin domains
Rwork0.20881 ---
obs0.21005 61256 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.754 Å2
Baniso -1Baniso -2Baniso -3
1--2.96 Å20 Å21.93 Å2
2--12.1 Å20 Å2
3----9.14 Å2
Refinement stepCycle: LAST / Resolution: 2.09→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7447 0 55 57 7559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197719
X-RAY DIFFRACTIONr_bond_other_d0.0050.026849
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.97410418
X-RAY DIFFRACTIONr_angle_other_deg1.345315886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.38623.605430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.63151233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1491567
X-RAY DIFFRACTIONr_chiral_restr0.0680.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218711
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021812
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_it0.7912.4013628
X-RAY DIFFRACTIONr_mcbond_other0.7912.4013627
X-RAY DIFFRACTIONr_mcangle_it1.3593.5974498
X-RAY DIFFRACTIONr_mcangle_other1.3593.5974499
X-RAY DIFFRACTIONr_scbond_it0.6612.4744091
X-RAY DIFFRACTIONr_scbond_other0.642.4574048
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0443.6545854
X-RAY DIFFRACTIONr_long_range_B_refined2.58718.8078127
X-RAY DIFFRACTIONr_long_range_B_other2.57918.8028123
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)
11A32550.1
12B32550.1
21A32680.09
22C32680.09
31A33910.07
32D33910.07
41A32400.06
42E32400.06
51A32120.08
52F32120.08
61A32690.08
62G32690.08
71A33410.07
72H33410.07
81A33380.08
82I33380.08
91A32740.07
92J32740.07
101A32920.07
102K32920.07
111A33110.07
112L33110.07
121B32330.11
122C32330.11
131B33640.08
132D33640.08
141B31210.08
142E31210.08
151B32260.09
152F32260.09
161B32120.1
162G32120.1
171B33900.08
172H33900.08
181B33520.09
182I33520.09
191B32700.09
192J32700.09
201B32590.08
202K32590.08
211B33030.08
212L33030.08
221C33820.08
222D33820.08
231C32260.07
232E32260.07
241C32310.1
242F32310.1
251C33150.1
252G33150.1
261C32900.09
262H32900.09
271C33830.08
272I33830.08
281C33060.08
282J33060.08
291C33660.08
292K33660.08
301C33560.09
302L33560.09
311D32370.05
312E32370.05
321D34140.07
322F34140.07
331D34270.07
332G34270.07
341D36050.08
342H36050.08
351D34820.05
352I34820.05
361D34900.05
362J34900.05
371D34310.06
372K34310.06
381D35380.04
382L35380.04
391E31470.06
392F31470.06
401E32020.06
402G32020.06
411E32030.06
412H32030.06
421E32080.06
422I32080.06
431E32190.06
432J32190.06
441E32340.05
442K32340.05
451E32350.05
452L32350.05
461F32860.09
462G32860.09
471F33980.06
472H33980.06
481F32820.07
482I32820.07
491F34290.07
492J34290.07
501F32830.08
502K32830.08
511F34210.06
512L34210.06
521G33480.09
522H33480.09
531G33290.07
532I33290.07
541G33660.08
542J33660.08
551G33580.08
552K33580.08
561G33960.08
562L33960.08
571H33850.07
572I33850.07
581H34450.08
582J34450.08
591H33400.08
592K33400.08
601H34760.06
602L34760.06
611I33520.05
612J33520.05
621I33860.05
622K33860.05
631I34090.05
632L34090.05
641J33790.07
642K33790.07
651J35340.07
652L35340.07
661K34040.06
662L34040.06
671M5190.19
672Q5190.19
681M5290.19
682S5290.19
691M5260.17
692U5260.17
701M5340.18
702W5340.18
711Q6290.21
712S6290.21
721Q5860.16
722U5860.16
731Q5800.19
732W5800.19
741S5460.23
742U5460.23
751S5680.18
752W5680.18
761U5870.19
762W5870.19
LS refinement shellResolution: 2.088→2.142 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 180 -
Rwork0.314 3710 -
obs--81.81 %
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)
10.8066-0.8015-0.72473.7443-0.04122.026-0.0398-0.01480.053-0.0108-0.0846-0.2733-0.20470.00380.12440.0956-0.0138-0.09640.16760.02020.1744-15.0269-1.6782-42.5995
21.63590.62220.03412.04060.08251.2325-0.1134-0.1557-0.2730.11710.1285-0.1671-0.1353-0.0387-0.01510.04410.0173-0.02040.18950.02460.2867-7.1617-21.4534-35.0444
31.99450.5329-0.09830.52120.29762.42460.0061-0.04430.22270.00770.02550.08330.0770.0248-0.03160.0499-0.0296-0.06880.1697-0.00180.25247.0165-14.2673-66.1474
40.24970.169-0.10770.96470.60173.1630.07960.0012-0.00890.0780.00550.03960.02970.1064-0.08510.04690.0137-0.07140.1956-0.01670.2399-14.1562-17.7024-74.3134
52.3833-2.242-0.13172.39010.48382.4186-0.1177-0.17040.13580.22190.08-0.3398-0.07240.07050.03770.0807-0.0032-0.1390.24990.0060.2454-9.925-12.8072-11.1821
60.9074-0.3021-0.27932.35660.02613.69040.0907-0.18940.1578-0.13420.04770.1033-0.0616-0.0039-0.13840.077-0.0053-0.09210.1453-0.04110.2056-22.50153.4984-19.2653
73.4862-0.4671-1.04491.18610.25171.9930.0783-0.0254-0.05350.2234-0.04830.2121-0.0268-0.092-0.030.07330.0129-0.01440.1952-0.00870.21979.160612.2695-11.746
81.9245-0.8841-1.32860.9036-0.40733.10660.0524-0.1283-0.0799-0.05550.04610.04770.00570.061-0.09850.088-0.0052-0.07940.15750.04360.258823.1886-4.0841-20.699
91.9661-0.43010.14770.5706-0.68530.94480.0280.0095-0.1730.04920.005-0.0087-0.0235-0.0408-0.03310.085-0.0643-0.09930.2006-0.00260.2239-5.610214.4468-65.9702
101.473-0.0519-0.15131.24520.10172.12030.2316-0.00770.1121-0.1045-0.0701-0.02820.0593-0.1428-0.16160.08910.0093-0.080.2210.01440.230815.274517.9359-75.0294
110.69670.1148-0.05513.584-0.83622.37080.02780.043-0.0227-0.1506-0.04020.17240.1695-0.02350.01240.063-0.0183-0.09350.18940.00690.187616.10051.8518-43.3338
121.3795-0.64290.31881.7190.22263.2297-0.136-0.10160.3579-0.02270.18320.12810.18290.0351-0.04720.05480.0144-0.11580.2274-0.01150.29118.612821.6314-34.5427
135.14770.7911-5.19980.3054-1.47257.7292-0.07-0.0994-0.1697-0.0193-0.0121-0.00690.07120.05150.08210.1641-0.0079-0.02270.1439-0.01970.197-26.3381-6.3243-45.6399
144.89776.4133-2.880510.7971-1.4683.91020.19840.0244-0.01710.1695-0.0428-0.2223-0.1922-0.1095-0.15550.04170.03370.06480.143-0.00780.34664.0768-22.6982-39.9828
150.5697-0.56410.06820.7649-0.10530.0157-0.0908-0.0068-0.25970.16660.10140.0611-0.0232-0.029-0.01060.07280.05-0.08080.3079-0.02510.3829.4717-28.1443-64.7103
161.16331.1011-1.87822.69940.86937.2859-0.05370.27240.0814-0.00420.3587-0.04290.0614-0.2817-0.3050.12560.0241-0.11090.18310.00490.1827-21.276-12.3051-64.7231
171.62132.01383.21912.54024.11657.32810.0311-0.02090.12650.0923-0.00980.16460.1201-0.067-0.02130.14250.05760.00490.1619-0.00810.2236-18.1162-19.4987-6.1106
182.75930.60710.99341.1224-0.76461.3374-0.23540.1874-0.258-0.37930.0418-0.3470.24310.03120.19360.2197-0.0115-0.010.2697-0.07130.2939-20.678812.2878-11.3293
191.86981.1293-2.80641.6347-2.6255.1225-0.0391-0.30320.058-0.01260.0084-0.07620.050.28470.03070.16440.0092-0.0670.1756-0.01540.144418.259918.741-6.0808
2010.12463.9751.90486.4314.74923.6495-0.4650.07310.24240.1720.33650.15780.20820.26540.12850.14680.0445-0.05710.11470.03610.178526.5917-12.2273-10.0194
212.7769-1.4299-0.07797.0294-5.56314.99190.2876-0.21640.06480.73180.08790.3868-0.78850.0416-0.37550.2292-0.0032-0.0350.1956-0.03620.1598-7.617926.2494-61.4544
222.75641.1532-0.63097.8657-1.30880.29240.02050.1291-0.08880.292-0.02560.0827-0.0468-0.02340.0050.09430.0464-0.09470.19640.02340.168323.349314.4918-65.8785
231.51312.10682.0253.42493.65634.13540.01960.18780.0936-0.2260.2535-0.0992-0.40280.2427-0.27310.1549-0.02010.0570.26660.05770.28127.17856.1888-47.6818
248.42290.2337-3.88150.0979-0.65975.1767-0.1812-0.6687-0.195-0.0323-0.0439-0.04580.26390.30330.22510.05030.0327-0.07480.18210.05520.2811.649327.1826-43.7169
2500000000000000-00.1042000.104200.1042000
2600000000000000-00.1042000.104200.1042000
2700000000000000-00.1042000.104200.1042000
2800000000000000-00.1042000.104200.1042000
2900000000000000-00.1042000.104200.1042000
3000000000000000-00.1042000.104200.1042000
3100000000000000-00.1042000.104200.1042000
3200000000000000-00.1042000.104200.1042000
3300000000000000-00.1042000.104200.1042000
3400000000000000-00.1042000.104200.1042000
3500000000000000-00.1042000.104200.1042000
3600000000000000-00.1042000.104200.1042000
3700000000000000-00.1042000.104200.1042000
3800000000000000-00.1042000.104200.1042000
3900000000000000-00.1042000.104200.1042000
4000000000000000-00.1042000.104200.1042000
4100000000000000-00.1042000.104200.1042000
4200000000000000-00.1042000.104200.1042000
4300000000000000-00.1042000.104200.1042000
4400000000000000-00.1042000.104200.1042000
4500000000000000-00.1042000.104200.1042000
4600000000000000-00.1042000.104200.1042000
4700000000000000-00.1042000.104200.1042000
4800000000000000-00.1042000.104200.1042000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1318 - 1382
2X-RAY DIFFRACTION2B1317 - 1382
3X-RAY DIFFRACTION3C1317 - 1381
4X-RAY DIFFRACTION4D1313 - 1382
5X-RAY DIFFRACTION5E1319 - 1381
6X-RAY DIFFRACTION6F1314 - 1380
7X-RAY DIFFRACTION7G1315 - 1381
8X-RAY DIFFRACTION8H1313 - 1382
9X-RAY DIFFRACTION9I1317 - 1382
10X-RAY DIFFRACTION10J1314 - 1381
11X-RAY DIFFRACTION11K1316 - 1381
12X-RAY DIFFRACTION12L1314 - 1381
13X-RAY DIFFRACTION13M153 - 164
14X-RAY DIFFRACTION14N155 - 159
15X-RAY DIFFRACTION15O154 - 164
16X-RAY DIFFRACTION16P152 - 159
17X-RAY DIFFRACTION17Q151 - 164
18X-RAY DIFFRACTION18R153 - 159
19X-RAY DIFFRACTION19S151 - 164
20X-RAY DIFFRACTION20T152 - 156
21X-RAY DIFFRACTION21U152 - 164
22X-RAY DIFFRACTION22V152 - 158
23X-RAY DIFFRACTION23W152 - 164
24X-RAY DIFFRACTION24X152 - 158
25X-RAY DIFFRACTION25A1318 - 1382
26X-RAY DIFFRACTION26B1317 - 1382
27X-RAY DIFFRACTION27C1317 - 1381
28X-RAY DIFFRACTION28D1313 - 1382
29X-RAY DIFFRACTION29E1319 - 1381
30X-RAY DIFFRACTION30F1314 - 1380
31X-RAY DIFFRACTION31G1315 - 1381
32X-RAY DIFFRACTION32H1313 - 1382
33X-RAY DIFFRACTION33I1317 - 1382
34X-RAY DIFFRACTION34J1314 - 1381
35X-RAY DIFFRACTION35K1316 - 1381
36X-RAY DIFFRACTION36L1314 - 1381
37X-RAY DIFFRACTION37M153 - 164
38X-RAY DIFFRACTION38N155 - 159
39X-RAY DIFFRACTION39O154 - 164
40X-RAY DIFFRACTION40P152 - 159
41X-RAY DIFFRACTION41Q151 - 164
42X-RAY DIFFRACTION42R153 - 159
43X-RAY DIFFRACTION43S151 - 164
44X-RAY DIFFRACTION44T152 - 156
45X-RAY DIFFRACTION45U152 - 164
46X-RAY DIFFRACTION46V152 - 158
47X-RAY DIFFRACTION47W152 - 164
48X-RAY DIFFRACTION48X152 - 158

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