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- PDB-5mu0: ACC1 Fab fragment in complex with citrullinated C1 epitope of CII... -

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Basic information

Entry
Database: PDB / ID: 5mu0
TitleACC1 Fab fragment in complex with citrullinated C1 epitope of CII (IA03)
Components
  • IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
  • heavy chain of ACC1 antibody Fab fragment
  • light chain of ACC1 antibody Fab fragment
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody (ACPA) Fab fragment collagen type II citrullinated C1 epitope
Function / homology
Function and homology information


Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / MET activates PTK2 signaling ...Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / MET activates PTK2 signaling / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / embryonic skeletal joint morphogenesis / otic vesicle development / ECM proteoglycans / limb bud formation / proteoglycan metabolic process / limb morphogenesis / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Integrin cell surface interactions / notochord development / cartilage development involved in endochondral bone morphogenesis / MHC class II protein binding / cellular response to BMP stimulus / tissue homeostasis / endochondral ossification / collagen trimer / skeletal system morphogenesis / collagen fibril organization / cartilage development / proteoglycan binding / inner ear morphogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cartilage condensation / roof of mouth development / inner ear development / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / extracellular matrix / ossification / skeletal system development / central nervous system development / sensory perception of sound / bone development / regulation of gene expression / collagen-containing extracellular matrix / protein homodimerization activity / extracellular space / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(II) chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDobritzsch, D. / Holmdahl, R. / Ge, C.
Funding support Sweden, 8items
OrganizationGrant numberCountry
Swedish Foundation for Strategic ResearchRBa08-0047 Sweden
Swedish Foundation for Strategic ResearchRB13-015 Sweden
Knut and Alice Wallenberg FoundationKAW 2010.0148 Sweden
Swedish Research CouncilK2009-75SX-21029-01-3 Sweden
Swedish Research CouncilK2012-75SX-22072-01-3 Sweden
Swedish Research CouncilK2011-52X-07931-25-5 Sweden
Swedish Research Council2015-02662 Sweden
European UnionIMI 115142
CitationJournal: JCI Insight / Year: 2017
Title: Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage.
Authors: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. ...Authors: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. / Burkhardt, H. / Dobritzsch, D. / Holmdahl, R.
History
DepositionJan 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / refine_hist
Item: _pdbx_audit_support.funding_organization / _refine_hist.d_res_low
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: heavy chain of ACC1 antibody Fab fragment
B: light chain of ACC1 antibody Fab fragment
C: heavy chain of ACC1 antibody Fab fragment
D: light chain of ACC1 antibody Fab fragment
E: heavy chain of ACC1 antibody Fab fragment
F: light chain of ACC1 antibody Fab fragment
G: heavy chain of ACC1 antibody Fab fragment
H: light chain of ACC1 antibody Fab fragment
I: heavy chain of ACC1 antibody Fab fragment
J: light chain of ACC1 antibody Fab fragment
K: heavy chain of ACC1 antibody Fab fragment
L: light chain of ACC1 antibody Fab fragment
M: heavy chain of ACC1 antibody Fab fragment
N: light chain of ACC1 antibody Fab fragment
O: heavy chain of ACC1 antibody Fab fragment
P: light chain of ACC1 antibody Fab fragment
Q: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
R: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
S: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
T: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
U: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
V: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
W: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II
X: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)390,03324
Polymers390,03324
Non-polymers00
Water1,44180
1
A: heavy chain of ACC1 antibody Fab fragment
B: light chain of ACC1 antibody Fab fragment
Q: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-26 kcal/mol
Surface area19580 Å2
MethodPISA
2
C: heavy chain of ACC1 antibody Fab fragment
D: light chain of ACC1 antibody Fab fragment
R: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-28 kcal/mol
Surface area19510 Å2
MethodPISA
3
E: heavy chain of ACC1 antibody Fab fragment
F: light chain of ACC1 antibody Fab fragment
S: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-26 kcal/mol
Surface area19780 Å2
MethodPISA
4
G: heavy chain of ACC1 antibody Fab fragment
H: light chain of ACC1 antibody Fab fragment
T: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-26 kcal/mol
Surface area19710 Å2
MethodPISA
5
I: heavy chain of ACC1 antibody Fab fragment
J: light chain of ACC1 antibody Fab fragment
U: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-26 kcal/mol
Surface area19590 Å2
MethodPISA
6
K: heavy chain of ACC1 antibody Fab fragment
L: light chain of ACC1 antibody Fab fragment
V: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-25 kcal/mol
Surface area19760 Å2
MethodPISA
7
M: heavy chain of ACC1 antibody Fab fragment
N: light chain of ACC1 antibody Fab fragment
W: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-27 kcal/mol
Surface area19320 Å2
MethodPISA
8
O: heavy chain of ACC1 antibody Fab fragment
P: light chain of ACC1 antibody Fab fragment
X: IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-24 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.147, 93.052, 121.751
Angle α, β, γ (deg.)92.75, 106.45, 104.37
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14A
24I
15A
25K
16A
26M
17A
27O
18B
28D
19B
29F
110B
210H
111B
211J
112B
212L
113B
213N
114B
214P
115C
215E
116C
216G
117C
217I
118C
218K
119C
219M
120C
220O
121D
221F
122D
222H
123D
223J
124D
224L
125D
225N
126D
226P
127E
227G
128E
228I
129E
229K
130E
230M
131E
231O
132F
232H
133F
233J
134F
234L
135F
235N
136F
236P
137G
237I
138G
238K
139G
239M
140G
240O
141H
241J
142H
242L
143H
243N
144H
244P
145I
245K
146I
246M
147I
247O
148J
248L
149J
249N
150J
250P
151K
251M
152K
252O
153L
253N
154L
254P
155M
255O
156N
256P

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
11GLUGLUGLUGLUAA1 - 2141 - 214
21GLUGLUGLUGLUCC1 - 2141 - 214
12GLUGLUGLYGLYAA1 - 2171 - 217
22GLUGLUGLYGLYEE1 - 2171 - 217
13GLUGLUGLYGLYAA1 - 2171 - 217
23GLUGLUGLYGLYGG1 - 2171 - 217
14GLUGLUGLYGLYAA1 - 2171 - 217
24GLUGLUGLYGLYII1 - 2171 - 217
15GLUGLUARGARGAA1 - 2161 - 216
25GLUGLUARGARGKK1 - 2161 - 216
16GLUGLUGLUGLUAA1 - 2141 - 214
26GLUGLUGLUGLUMM1 - 2141 - 214
17VALVALPROPROAA2 - 2152 - 215
27VALVALPROPROOO2 - 2152 - 215
18ASPASPGLUGLUBB1 - 2171 - 217
28ASPASPGLUGLUDD1 - 2171 - 217
19ASPASPARGARGBB1 - 2151 - 215
29ASPASPARGARGFF1 - 2151 - 215
110ASPASPGLUGLUBB1 - 2171 - 217
210ASPASPGLUGLUHH1 - 2171 - 217
111ASPASPGLUGLUBB1 - 2171 - 217
211ASPASPGLUGLUJJ1 - 2171 - 217
112ASPASPGLUGLUBB1 - 2171 - 217
212ASPASPGLUGLULL1 - 2171 - 217
113ASPASPASNASNBB1 - 2141 - 214
213ASPASPASNASNNN1 - 2141 - 214
114ASPASPARGARGBB1 - 2151 - 215
214ASPASPARGARGPP1 - 2151 - 215
115GLUGLUPROPROCC1 - 2151 - 215
215GLUGLUPROPROEE1 - 2151 - 215
116GLUGLUGLUGLUCC1 - 2141 - 214
216GLUGLUGLUGLUGG1 - 2141 - 214
117GLUGLUGLUGLUCC1 - 2141 - 214
217GLUGLUGLUGLUII1 - 2141 - 214
118GLUGLUGLUGLUCC1 - 2141 - 214
218GLUGLUGLUGLUKK1 - 2141 - 214
119GLUGLUPROPROCC1 - 2151 - 215
219GLUGLUPROPROMM1 - 2151 - 215
120VALVALPROPROCC2 - 2152 - 215
220VALVALPROPROOO2 - 2152 - 215
121ASPASPARGARGDD1 - 2151 - 215
221ASPASPARGARGFF1 - 2151 - 215
122ASPASPGLUGLUDD1 - 2171 - 217
222ASPASPGLUGLUHH1 - 2171 - 217
123ASPASPGLUGLUDD1 - 2171 - 217
223ASPASPGLUGLUJJ1 - 2171 - 217
124ASPASPGLUGLUDD1 - 2171 - 217
224ASPASPGLUGLULL1 - 2171 - 217
125ASPASPASNASNDD1 - 2141 - 214
225ASPASPASNASNNN1 - 2141 - 214
126ASPASPARGARGDD1 - 2151 - 215
226ASPASPARGARGPP1 - 2151 - 215
127GLUGLUGLYGLYEE1 - 2171 - 217
227GLUGLUGLYGLYGG1 - 2171 - 217
128GLUGLUPROPROEE1 - 2181 - 218
228GLUGLUPROPROII1 - 2181 - 218
129GLUGLUPROPROEE1 - 2181 - 218
229GLUGLUPROPROKK1 - 2181 - 218
130GLUGLUPROPROEE1 - 2151 - 215
230GLUGLUPROPROMM1 - 2151 - 215
131VALVALGLUGLUEE2 - 2142 - 214
231VALVALGLUGLUOO2 - 2142 - 214
132ASPASPARGARGFF1 - 2151 - 215
232ASPASPARGARGHH1 - 2151 - 215
133ASPASPARGARGFF1 - 2151 - 215
233ASPASPARGARGJJ1 - 2151 - 215
134ASPASPARGARGFF1 - 2151 - 215
234ASPASPARGARGLL1 - 2151 - 215
135ASPASPASNASNFF1 - 2141 - 214
235ASPASPASNASNNN1 - 2141 - 214
136ASPASPASNASNFF1 - 2161 - 216
236ASPASPASNASNPP1 - 2161 - 216
137GLUGLUARGARGGG1 - 2161 - 216
237GLUGLUARGARGII1 - 2161 - 216
138GLUGLUGLYGLYGG1 - 2171 - 217
238GLUGLUGLYGLYKK1 - 2171 - 217
139GLUGLUGLUGLUGG1 - 2141 - 214
239GLUGLUGLUGLUMM1 - 2141 - 214
140VALVALPROPROGG2 - 2152 - 215
240VALVALPROPROOO2 - 2152 - 215
141ASPASPGLUGLUHH1 - 2171 - 217
241ASPASPGLUGLUJJ1 - 2171 - 217
142ASPASPGLUGLUHH1 - 2171 - 217
242ASPASPGLUGLULL1 - 2171 - 217
143ASPASPASNASNHH1 - 2141 - 214
243ASPASPASNASNNN1 - 2141 - 214
144ASPASPARGARGHH1 - 2151 - 215
244ASPASPARGARGPP1 - 2151 - 215
145GLUGLUPROPROII1 - 2181 - 218
245GLUGLUPROPROKK1 - 2181 - 218
146GLUGLUGLUGLUII1 - 2141 - 214
246GLUGLUGLUGLUMM1 - 2141 - 214
147VALVALGLUGLUII2 - 2142 - 214
247VALVALGLUGLUOO2 - 2142 - 214
148ASPASPGLUGLUJJ1 - 2171 - 217
248ASPASPGLUGLULL1 - 2171 - 217
149ASPASPASNASNJJ1 - 2141 - 214
249ASPASPASNASNNN1 - 2141 - 214
150ASPASPARGARGJJ1 - 2151 - 215
250ASPASPARGARGPP1 - 2151 - 215
151GLUGLUGLUGLUKK1 - 2141 - 214
251GLUGLUGLUGLUMM1 - 2141 - 214
152VALVALPROPROKK2 - 2152 - 215
252VALVALPROPROOO2 - 2152 - 215
153ASPASPASNASNLL1 - 2141 - 214
253ASPASPASNASNNN1 - 2141 - 214
154ASPASPARGARGLL1 - 2151 - 215
254ASPASPARGARGPP1 - 2151 - 215
155VALVALPROPROMM2 - 2152 - 215
255VALVALPROPROOO2 - 2152 - 215
156ASPASPASNASNNN1 - 2141 - 214
256ASPASPASNASNPP1 - 2141 - 214

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

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Components

#1: Antibody
heavy chain of ACC1 antibody Fab fragment


Mass: 23353.164 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma / Variant: B10.RIII.Cia5
#2: Antibody
light chain of ACC1 antibody Fab fragment


Mass: 23721.199 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma / Variant: B10.RIII.Cia5
#3: Protein/peptide
IA03 peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,IA03 peptide containing the citrullinated C1 epitope of collagen type II / Alpha-1 type II collagen


Mass: 1679.770 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: the C-terminus is aminated / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P28481
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 16% (w/v) PEG 8000, 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→78.15 Å / Num. obs: 87706 / % possible obs: 90.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.077 / Net I/σ(I): 20.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 4457 / Rpim(I) all: 0.553 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OR9

2or9


Resolution: 2.7→78.15 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.896 / SU B: 49.851 / SU ML: 0.427 / Cross valid method: THROUGHOUT / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27877 4339 5 %RANDOM
Rwork0.25212 ---
obs0.25347 82058 89.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.461 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å2-1.02 Å2-0.95 Å2
2---1.8 Å22.33 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.7→78.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26700 0 0 80 26780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227343
X-RAY DIFFRACTIONr_bond_other_d0.0030.0225009
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.94537130
X-RAY DIFFRACTIONr_angle_other_deg1.702357892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43853492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26824.4541071
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.747154315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.63615109
X-RAY DIFFRACTIONr_chiral_restr0.0990.24170
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02130772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026081
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_it1.1383.15114067
X-RAY DIFFRACTIONr_mcbond_other1.1383.1514066
X-RAY DIFFRACTIONr_mcangle_it1.9944.71717526
X-RAY DIFFRACTIONr_mcangle_other1.9944.71817527
X-RAY DIFFRACTIONr_scbond_it0.8473.20813276
X-RAY DIFFRACTIONr_scbond_other0.8473.20913277
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4914.77919605
X-RAY DIFFRACTIONr_long_range_B_refined3.09335.0527537
X-RAY DIFFRACTIONr_long_range_B_other3.09335.05227538
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)
11A124760.07
12C124760.07
21A126700.07
22E126700.07
31A126620.06
32G126620.06
41A126300.08
42I126300.08
51A125920.07
52K125920.07
61A125280.06
62M125280.06
71A122960.08
72O122960.08
81B128820.07
82D128820.07
91B129380.05
92F129380.05
101B128620.07
102H128620.07
111B128400.07
112J128400.07
121B128220.07
122L128220.07
131B126780.08
132N126780.08
141B128000.08
142P128000.08
151C125700.07
152E125700.07
161C124960.07
162G124960.07
171C124540.08
172I124540.08
181C124900.07
182K124900.07
191C125840.07
192M125840.07
201C123280.08
202O123280.08
211D129480.06
212F129480.06
221D129000.07
222H129000.07
231D129480.07
232J129480.07
241D128720.07
242L128720.07
251D127640.07
252N127640.07
261D128920.07
262P128920.07
271E126800.07
272G126800.07
281E126800.07
282I126800.07
291E126260.08
292K126260.08
301E125600.07
302M125600.07
311E123620.08
312O123620.08
321F128940.06
322H128940.06
331F128980.06
332J128980.06
341F128580.07
342L128580.07
351F128280.07
352N128280.07
361F129980.07
362P129980.07
371G126560.07
372I126560.07
381G126180.07
382K126180.07
391G125180.07
392M125180.07
401G123580.07
402O123580.07
411H128440.08
412J128440.08
421H128540.08
422L128540.08
431H126980.07
432N126980.07
441H128580.07
442P128580.07
451I125700.08
452K125700.08
461I124600.08
462M124600.08
471I122620.08
472O122620.08
481J128280.07
482L128280.07
491J126420.08
492N126420.08
501J127640.08
502P127640.08
511K123960.08
512M123960.08
521K122420.09
522O122420.09
531L126340.08
532N126340.08
541L127960.08
542P127960.08
551M123080.09
552O123080.09
561N128000.06
562P128000.06
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 295 -
Rwork0.412 5842 -
obs--85.76 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4572-0.8648-0.60085.22261.64047.0138-0.2305-0.2305-0.09320.2147-0.02270.15430.1276-0.42230.25320.1133-0.11330.05590.2371-0.05470.040222.8342-9.4498-18.3049
22.751-1.5936-0.09915.8169-0.33520.29460.2161-0.1940.47940.7815-0.4806-0.020.0703-0.06310.26450.2814-0.11110.24310.4901-0.17680.39364.848413.1901-8.0265
34.1701-0.103-1.23397.3542-1.3271.6379-0.0352-0.04650.08790.0721-0.12750.7085-0.1185-0.18960.16270.1764-0.08540.12860.3118-0.22290.33051.858315.091-14.1114
44.1797-1.54210.06146.36830.33972.21730.03590.36350.25-0.2619-0.255-0.5047-0.2282-0.12430.21910.1774-0.08990.09610.2194-0.01040.162533.44498.4274-27.3123
54.3169-0.1214-2.17622.86110.15773.0745-0.0052-0.47160.42320.7255-0.29620.0125-0.1273-0.01650.30140.3028-0.06510.11330.3779-0.1750.391510.867128.4854-7.9331
61.81691.9777-0.93595.9155-2.19752.22160.10630.1236-0.0529-0.4185-0.2798-0.65150.12340.54520.17350.20560.06590.1860.3568-0.03760.235785.22325.8046-39.0705
73.27070.68080.6879.3444-1.35192.39440.0994-0.2178-0.15430.19490.11050.4750.1563-0.2002-0.20990.087-0.06790.07020.1065-0.03890.119862.759210.859-30.9065
84.2934-1.3235-2.40911.5611-0.00864.31080.27080.61810.1663-0.8017-0.3506-0.22220.31760.38270.07980.65410.0250.31960.3381-0.05850.249583.852628.9132-53.5213
92.5616-2.3795-0.41053.25581.20511.64880.26050.45560.225-0.399-0.3267-0.18620.16280.09510.06620.3438-0.11180.15480.42830.11320.263647.3718-17.9656-82.3056
102.4619-2.0792-0.42213.3570.18732.78820.15220.16970.02280.106-0.1753-0.17780.0910.11440.02310.253-0.17890.05790.2171-0.02810.155147.6344-32.1613-70.074
115.94530.8290.3982.1632-0.45424.29110.16850.2745-0.1329-0.0306-0.03930.1520.36510.0857-0.12920.339-0.02950.0430.0635-0.05390.054858.702-35.0893-54.259
126.011-1.49212.15721.696-0.68454.3497-0.13730.38170.2873-0.199-0.0966-0.27760.17480.1960.23380.293-0.14280.16970.1048-0.05720.124690.325-36.9477-47.7411
134.7365-0.05580.02321.3397-0.1931.3795-0.1104-0.4178-0.08630.1669-0.03930.2321-0.1085-0.35310.14970.2551-0.05820.12070.1647-0.08630.111267.4733-26.9529-34.8801
145.97690.1636-3.57671.4617-0.28114.00870.10370.19230.6318-0.17970.1104-0.1832-0.37330.114-0.21410.3122-0.03770.04790.147-0.0260.138494.7638-21.3496-40.0155
156.5297-1.13220.66043.4220.92714.0238-0.2103-0.45470.0961.30380.0716-0.51870.5303-0.09150.13870.5743-0.0255-0.1150.2904-0.00720.195745.5008-28.2127.1019
166.8757-0.23931.78591.9531-0.42511.9587-0.2283-0.892-0.2380.70630.20480.0671-0.0744-0.35210.02350.42050.06960.15180.33810.02970.103731.2295-31.06616.3825
1749.916827.19167.556816.51717.79649.11450.4668-0.841-0.59670.2895-0.5076-0.22390.064-0.2530.04070.4130.02310.10150.28230.12020.457313.4349-42.25899.9269
185.6282-0.1631.01592.5254-1.02972.9666-0.23810.066-0.02020.01710.16460.2027-0.0546-0.15660.07350.1871-0.01650.16020.0836-0.00750.169527.1126-26.9348-10.4403
196.3574-5.4189-0.75578.32643.76756.6863-0.10041.05890.55510.0165-0.0621-0.4957-0.29650.51140.16250.4578-0.1548-0.05870.4980.0280.32260.294127.0655-59.5747
205.45330.09696.07623.18512.802712.0073-0.08940.65630.17560.31850.0633-0.15310.78530.80230.02610.2621-0.01550.06860.2664-0.03140.106556.622518.2231-51.5225
210.2229-0.08610.01730.6802-0.0027.2127-0.07510.21830.1414-0.3540.0219-0.199-0.09261.30190.05320.4035-0.12180.14660.696-0.02050.315158.200222.6554-77.5191
227.40830.97445.4032.17861.78479.83550.1946-0.94280.150.5611-0.24060.53340.0685-1.51930.0460.2099-0.0430.22050.3315-0.05080.240937.450115.3057-59.1082
235.1931-0.8726-3.05311.80520.69015.354-0.11680.1258-0.3936-0.2961-0.004-0.11670.54190.71870.12070.37650.02860.08920.4918-0.01090.142148.934310.5305-92.6691
243.5223-0.2898-1.92438.2026-0.36846.1157-0.2785-0.18190.1316-0.0326-0.11350.2921-0.471-0.27650.3920.2048-0.081-0.03190.3110.03430.339936.500527.4271-7.737
250.5033-0.6180.12613.10253.32225.6405-0.2878-0.36410.10940.75030.18070.06390.0044-0.40380.10710.75690.00740.12710.51360.13580.631837.101934.695414.044
264.7205-0.43083.62792.5888-0.40276.7077-0.07930.4276-0.2144-0.46890.4178-1.4253-0.27820.93-0.33850.1214-0.09330.31930.4157-0.17130.944957.633825.2475-3.6738
271.22450.02610.27311.64780.07273.45280.1047-0.4263-0.19261.20740.1975-0.0934-0.09830.0235-0.30220.92880.08550.06380.6532-0.00230.658749.07228.495430.5771
281.65310.60461.65326.9043-0.33355.3351-0.5076-0.68460.67941.29790.5629-0.0738-0.5664-0.756-0.05530.6340.3346-0.18380.7244-0.03220.943360.63629.636719.0187
294.21913.2509-0.62922.5801-0.30044.27060.9472-0.19860.36930.9175-0.08720.2422-1.2969-0.9612-0.861.3670.38820.30471.3130.26930.662855.0976-11.93440.1853
304.9861-3.13311.70588.8946-2.57653.98590.18670.8450.4765-0.5259-0.3048-1.06990.12040.76870.11810.213-0.10180.0470.57850.1870.504769.2984-9.17948.8828
316.2494-0.9296-4.4271.59891.65844.4524-0.05420.47470.09620.51490.0320.44030.08-1.0430.02220.81310.15950.08711.12240.37350.544349.2725-25.667933.8395
321.7727-0.9938-2.706817.0839-2.73685.23390.03220.17820.0675-0.37760.0558-0.01510.0759-0.3063-0.0880.19740.00080.1320.3554-0.01010.149633.5842-8.1051-31.9189
330.1027-0.02590.22120.0188-0.03610.57360.07370.0429-0.12440.0310.02390.08460.14330.1882-0.09750.4409-0.0060.05170.36860.05970.524465.1816-3.5356-22.2479
341.09982.5439-0.93877.9292-2.26280.806-0.1087-0.01040.20590.59650.26440.4640.0555-0.0049-0.15570.38810.0247-0.01910.40240.00860.543426.5904-8.0348-66.3412
356.94380.99258.40140.17031.204210.3473-0.1514-1.27340.0402-0.0262-0.01920.0392-0.4047-1.56290.17060.49370.08180.13461.10320.17860.412846.4736-34.581-41.718
361.00280.35890.59330.13160.21070.35870.011-0.1345-0.02790.012-0.0243-0.0431-0.0389-0.05360.01330.3802-0.06030.00750.5012-0.02010.616959.1044-29.1769-5.3285
373.6056-2.44087.32489.2649-12.38922.1330.3862-1.28630.19-0.14290.05770.72470.6638-1.8229-0.4440.32880.01840.06040.652-0.1760.443844.327523.5229-45.9438
388.8051-0.9505-0.0499.444610.009210.72450.68681.5671-0.09391.5047-0.3695-0.27151.6336-0.1735-0.31730.6205-0.09320.11080.54850.05360.317349.062527.272-17.6114
393.0753-1.26410.006916.33513.82530.932-0.1195-0.186-0.42690.08060.2776-0.43450.0065-0.0055-0.15810.29690.00790.02190.58110.00780.539673.83927.64968.2414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2A109 - 149
3X-RAY DIFFRACTION3A150 - 217
4X-RAY DIFFRACTION4B1 - 109
5X-RAY DIFFRACTION5B110 - 213
6X-RAY DIFFRACTION6C1 - 215
7X-RAY DIFFRACTION7D1 - 107
8X-RAY DIFFRACTION8D108 - 213
9X-RAY DIFFRACTION9E1 - 215
10X-RAY DIFFRACTION10F1 - 213
11X-RAY DIFFRACTION11G1 - 111
12X-RAY DIFFRACTION12G112 - 215
13X-RAY DIFFRACTION13H1 - 141
14X-RAY DIFFRACTION14H142 - 213
15X-RAY DIFFRACTION15I1 - 51
16X-RAY DIFFRACTION16I52 - 207
17X-RAY DIFFRACTION17I208 - 215
18X-RAY DIFFRACTION18J1 - 213
19X-RAY DIFFRACTION19K1 - 31
20X-RAY DIFFRACTION20K32 - 69
21X-RAY DIFFRACTION21K70 - 215
22X-RAY DIFFRACTION22L1 - 107
23X-RAY DIFFRACTION23L108 - 213
24X-RAY DIFFRACTION24M1 - 67
25X-RAY DIFFRACTION25M68 - 215
26X-RAY DIFFRACTION26N1 - 104
27X-RAY DIFFRACTION27N105 - 213
28X-RAY DIFFRACTION28O2 - 107
29X-RAY DIFFRACTION29O108 - 215
30X-RAY DIFFRACTION30P1 - 108
31X-RAY DIFFRACTION31P109 - 213
32X-RAY DIFFRACTION32Q3 - 13
33X-RAY DIFFRACTION33R4 - 13
34X-RAY DIFFRACTION34S4 - 13
35X-RAY DIFFRACTION35T4 - 13
36X-RAY DIFFRACTION36U4 - 13
37X-RAY DIFFRACTION37V4 - 13
38X-RAY DIFFRACTION38W5 - 13
39X-RAY DIFFRACTION39X4 - 13

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