[English] 日本語
Yorodumi
- PDB-5mu2: ACC1 Fab fragment in complex with CII583-591 (CG10) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mu2
TitleACC1 Fab fragment in complex with CII583-591 (CG10)
Components
  • ACC1 Fab fragment heavy chain
  • ACC1 Fab fragment light chain
  • synthetic peptide containing the CII583-591 epitope of collagen type II
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody (ACPA) Fab fragment collagen type II
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDobritzsch, D. / Holmdahl, R. / Ge, C.
Funding support Sweden, 6items
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 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 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACC1 Fab fragment heavy chain
B: ACC1 Fab fragment light chain
C: ACC1 Fab fragment heavy chain
D: ACC1 Fab fragment light chain
E: ACC1 Fab fragment heavy chain
F: ACC1 Fab fragment light chain
G: ACC1 Fab fragment heavy chain
H: ACC1 Fab fragment light chain
I: ACC1 Fab fragment heavy chain
J: ACC1 Fab fragment light chain
K: ACC1 Fab fragment heavy chain
L: ACC1 Fab fragment light chain
M: ACC1 Fab fragment heavy chain
N: ACC1 Fab fragment light chain
O: ACC1 Fab fragment heavy chain
P: ACC1 Fab fragment light chain
X: synthetic peptide containing the CII583-591 epitope of collagen type II
Q: synthetic peptide containing the CII583-591 epitope of collagen type II
R: synthetic peptide containing the CII583-591 epitope of collagen type II
S: synthetic peptide containing the CII583-591 epitope of collagen type II
T: synthetic peptide containing the CII583-591 epitope of collagen type II
U: synthetic peptide containing the CII583-591 epitope of collagen type II
V: synthetic peptide containing the CII583-591 epitope of collagen type II
W: synthetic peptide containing the CII583-591 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)398,18624
Polymers398,18624
Non-polymers00
Water7,945441
1
A: ACC1 Fab fragment heavy chain
B: ACC1 Fab fragment light chain
X: synthetic peptide containing the CII583-591 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-35 kcal/mol
Surface area19990 Å2
MethodPISA
2
C: ACC1 Fab fragment heavy chain
D: ACC1 Fab fragment light chain
Q: synthetic peptide containing the CII583-591 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-36 kcal/mol
Surface area20120 Å2
MethodPISA
3
E: ACC1 Fab fragment heavy chain
F: ACC1 Fab fragment light chain
R: synthetic peptide containing the CII583-591 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-32 kcal/mol
Surface area19930 Å2
MethodPISA
4
G: ACC1 Fab fragment heavy chain
H: ACC1 Fab fragment light chain
S: synthetic peptide containing the CII583-591 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-31 kcal/mol
Surface area19840 Å2
MethodPISA
5
I: ACC1 Fab fragment heavy chain
J: ACC1 Fab fragment light chain
T: synthetic peptide containing the CII583-591 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-36 kcal/mol
Surface area19880 Å2
MethodPISA
6
K: ACC1 Fab fragment heavy chain
L: ACC1 Fab fragment light chain
U: synthetic peptide containing the CII583-591 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-36 kcal/mol
Surface area19900 Å2
MethodPISA
7
M: ACC1 Fab fragment heavy chain
N: ACC1 Fab fragment light chain
V: synthetic peptide containing the CII583-591 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-37 kcal/mol
Surface area19780 Å2
MethodPISA
8
O: ACC1 Fab fragment heavy chain
P: ACC1 Fab fragment light chain
W: synthetic peptide containing the CII583-591 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-33 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.861, 156.008, 156.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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
157X
257Q
158X
258R
159X
259S
160X
260T
161X
261U
162X
262V
163Q
263R
164Q
264S
165Q
265T
166R
266S
167R
267T
168R
268U
169R
269V
170S
270T
171S
271U
172S
272V
173T
273U
174T
274V
175U
275V

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
11GLUGLUPROPROAA1 - 2181 - 218
21GLUGLUPROPROCC1 - 2181 - 218
12GLUGLUPROPROAA1 - 2181 - 218
22GLUGLUPROPROEE1 - 2181 - 218
13GLUGLUARGARGAA1 - 2161 - 216
23GLUGLUARGARGGG1 - 2161 - 216
14GLUGLUPROPROAA1 - 2181 - 218
24GLUGLUPROPROII1 - 2181 - 218
15GLUGLUPROPROAA1 - 2181 - 218
25GLUGLUPROPROKK1 - 2181 - 218
16GLUGLUPROPROAA1 - 2181 - 218
26GLUGLUPROPROMM1 - 2181 - 218
17GLUGLUGLYGLYAA1 - 2171 - 217
27GLUGLUGLYGLYOO1 - 2171 - 217
18ASPASPCYSCYSBB1 - 2181 - 218
28ASPASPCYSCYSDD1 - 2181 - 218
19ASPASPASNASNBB1 - 2161 - 216
29ASPASPASNASNFF1 - 2161 - 216
110ASPASPASNASNBB1 - 2161 - 216
210ASPASPASNASNHH1 - 2161 - 216
111ASPASPCYSCYSBB1 - 2181 - 218
211ASPASPCYSCYSJJ1 - 2181 - 218
112ASPASPCYSCYSBB1 - 2181 - 218
212ASPASPCYSCYSLL1 - 2181 - 218
113ASPASPCYSCYSBB1 - 2181 - 218
213ASPASPCYSCYSNN1 - 2181 - 218
114ASPASPASNASNBB1 - 2161 - 216
214ASPASPASNASNPP1 - 2161 - 216
115GLUGLUPROPROCC1 - 2181 - 218
215GLUGLUPROPROEE1 - 2181 - 218
116GLUGLUARGARGCC1 - 2161 - 216
216GLUGLUARGARGGG1 - 2161 - 216
117GLUGLUPROPROCC1 - 2181 - 218
217GLUGLUPROPROII1 - 2181 - 218
118GLUGLUPROPROCC1 - 2181 - 218
218GLUGLUPROPROKK1 - 2181 - 218
119GLUGLUPROPROCC1 - 2181 - 218
219GLUGLUPROPROMM1 - 2181 - 218
120GLUGLUGLYGLYCC1 - 2171 - 217
220GLUGLUGLYGLYOO1 - 2171 - 217
121ASPASPASNASNDD1 - 2161 - 216
221ASPASPASNASNFF1 - 2161 - 216
122ASPASPASNASNDD1 - 2161 - 216
222ASPASPASNASNHH1 - 2161 - 216
123ASPASPCYSCYSDD1 - 2181 - 218
223ASPASPCYSCYSJJ1 - 2181 - 218
124ASPASPCYSCYSDD1 - 2181 - 218
224ASPASPCYSCYSLL1 - 2181 - 218
125ASPASPCYSCYSDD1 - 2181 - 218
225ASPASPCYSCYSNN1 - 2181 - 218
126ASPASPASNASNDD1 - 2161 - 216
226ASPASPASNASNPP1 - 2161 - 216
127GLUGLUARGARGEE1 - 2161 - 216
227GLUGLUARGARGGG1 - 2161 - 216
128GLUGLUPROPROEE1 - 2181 - 218
228GLUGLUPROPROII1 - 2181 - 218
129GLUGLUPROPROEE1 - 2181 - 218
229GLUGLUPROPROKK1 - 2181 - 218
130GLUGLUPROPROEE1 - 2181 - 218
230GLUGLUPROPROMM1 - 2181 - 218
131GLUGLUARGARGEE1 - 2161 - 216
231GLUGLUARGARGOO1 - 2161 - 216
132ASPASPGLUGLUFF1 - 2171 - 217
232ASPASPGLUGLUHH1 - 2171 - 217
133ASPASPASNASNFF1 - 2161 - 216
233ASPASPASNASNJJ1 - 2161 - 216
134ASPASPASNASNFF1 - 2161 - 216
234ASPASPASNASNLL1 - 2161 - 216
135ASPASPASNASNFF1 - 2161 - 216
235ASPASPASNASNNN1 - 2161 - 216
136ASPASPGLUGLUFF1 - 2171 - 217
236ASPASPGLUGLUPP1 - 2171 - 217
137GLUGLUARGARGGG1 - 2161 - 216
237GLUGLUARGARGII1 - 2161 - 216
138GLUGLUARGARGGG1 - 2161 - 216
238GLUGLUARGARGKK1 - 2161 - 216
139GLUGLUARGARGGG1 - 2161 - 216
239GLUGLUARGARGMM1 - 2161 - 216
140GLUGLUARGARGGG1 - 2161 - 216
240GLUGLUARGARGOO1 - 2161 - 216
141ASPASPASNASNHH1 - 2161 - 216
241ASPASPASNASNJJ1 - 2161 - 216
142ASPASPASNASNHH1 - 2161 - 216
242ASPASPASNASNLL1 - 2161 - 216
143ASPASPASNASNHH1 - 2161 - 216
243ASPASPASNASNNN1 - 2161 - 216
144ASPASPGLUGLUHH1 - 2171 - 217
244ASPASPGLUGLUPP1 - 2171 - 217
145GLUGLUPROPROII1 - 2181 - 218
245GLUGLUPROPROKK1 - 2181 - 218
146GLUGLUPROPROII1 - 2181 - 218
246GLUGLUPROPROMM1 - 2181 - 218
147GLUGLUGLYGLYII1 - 2171 - 217
247GLUGLUGLYGLYOO1 - 2171 - 217
148ASPASPCYSCYSJJ1 - 2181 - 218
248ASPASPCYSCYSLL1 - 2181 - 218
149ASPASPCYSCYSJJ1 - 2181 - 218
249ASPASPCYSCYSNN1 - 2181 - 218
150ASPASPASNASNJJ1 - 2161 - 216
250ASPASPASNASNPP1 - 2161 - 216
151GLUGLUPROPROKK1 - 2181 - 218
251GLUGLUPROPROMM1 - 2181 - 218
152GLUGLUGLYGLYKK1 - 2171 - 217
252GLUGLUGLYGLYOO1 - 2171 - 217
153ASPASPCYSCYSLL1 - 2181 - 218
253ASPASPCYSCYSNN1 - 2181 - 218
154ASPASPASNASNLL1 - 2161 - 216
254ASPASPASNASNPP1 - 2161 - 216
155GLUGLUGLYGLYMM1 - 2171 - 217
255GLUGLUGLYGLYOO1 - 2171 - 217
156ASPASPASNASNNN1 - 2161 - 216
256ASPASPASNASNPP1 - 2161 - 216
157HYPHYPILEILEXQ9 - 219 - 21
257HYPHYPILEILEQR9 - 219 - 21
158HYPHYPPROPROXQ9 - 239 - 23
258HYPHYPPROPRORS9 - 239 - 23
159HYPHYPPROPROXQ9 - 239 - 23
259HYPHYPPROPROST9 - 239 - 23
160PROPROGLYGLYXQ11 - 2211 - 22
260PROPROGLYGLYTU11 - 2211 - 22
161HYPHYPGLYGLYXQ12 - 2212 - 22
261HYPHYPGLYGLYUV12 - 2212 - 22
162HYPHYPGLYGLYXQ12 - 2212 - 22
262HYPHYPGLYGLYVW12 - 2212 - 22
163HYPHYPILEILEQR9 - 219 - 21
263HYPHYPILEILERS9 - 219 - 21
164HYPHYPILEILEQR9 - 219 - 21
264HYPHYPILEILEST9 - 219 - 21
165PROPROILEILEQR11 - 2111 - 21
265PROPROILEILETU11 - 2111 - 21
166HYPHYPPROPRORS9 - 239 - 23
266HYPHYPPROPROST9 - 239 - 23
167PROPROGLYGLYRS11 - 2211 - 22
267PROPROGLYGLYTU11 - 2211 - 22
168HYPHYPGLYGLYRS12 - 2212 - 22
268HYPHYPGLYGLYUV12 - 2212 - 22
169HYPHYPGLYGLYRS12 - 2212 - 22
269HYPHYPGLYGLYVW12 - 2212 - 22
170PROPROGLYGLYST11 - 2211 - 22
270PROPROGLYGLYTU11 - 2211 - 22
171HYPHYPGLYGLYST12 - 2212 - 22
271HYPHYPGLYGLYUV12 - 2212 - 22
172HYPHYPGLYGLYST12 - 2212 - 22
272HYPHYPGLYGLYVW12 - 2212 - 22
173HYPHYPGLYGLYTU12 - 2212 - 22
273HYPHYPGLYGLYUV12 - 2212 - 22
174HYPHYPGLYGLYTU12 - 2212 - 22
274HYPHYPGLYGLYVW12 - 2212 - 22
175HYPHYPGLYGLYUV12 - 2212 - 22
275HYPHYPGLYGLYVW12 - 2212 - 22

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

-
Components

#1: Antibody
ACC1 Fab fragment heavy chain


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
ACC1 Fab fragment light chain


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
synthetic peptide containing the CII583-591 epitope of collagen type II


Mass: 2698.919 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: the synthesized peptide is a triple-helical homotrimer of the above provided sequence, but only a single alpha-chain is bound to ACC1 in the crystal structure
Source: (synth.) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% (w/v) PEG3350, 0.1 M Bistris-Propane pH 7.5, 0.2 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PILATUS 6 / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→49.09 Å / Num. obs: 100498 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4899 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MU0
Resolution: 2.7→49.09 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.92 / SU B: 31.297 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22845 4864 4.8 %RANDOM
Rwork0.20629 ---
obs0.20737 95561 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.939 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å2-0 Å2
2---0.57 Å20 Å2
3---0.77 Å2
Refinement stepCycle: 1 / Resolution: 2.7→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27006 0 0 441 27447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227684
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225288
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.94737631
X-RAY DIFFRACTIONr_angle_other_deg1.005358617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74353544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39924.4441080
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.918154355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.31515112
X-RAY DIFFRACTIONr_chiral_restr0.1110.24213
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02131216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026112
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_it0.8322.52614266
X-RAY DIFFRACTIONr_mcbond_other0.8322.52614265
X-RAY DIFFRACTIONr_mcangle_it1.4823.78417780
X-RAY DIFFRACTIONr_mcangle_other1.4813.78417781
X-RAY DIFFRACTIONr_scbond_it0.782.56813418
X-RAY DIFFRACTIONr_scbond_other0.782.56813419
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3543.82119852
X-RAY DIFFRACTIONr_long_range_B_refined2.70528.12627879
X-RAY DIFFRACTIONr_long_range_B_other2.70528.12627880
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)
11A128700.06
12C128700.06
21A128560.06
22E128560.06
31A127840.05
32G127840.05
41A129080.05
42I129080.05
51A129260.05
52K129260.05
61A129180.06
62M129180.06
71A128780.05
72O128780.05
81B133240.05
82D133240.05
91B133460.03
92F133460.03
101B132760.05
102H132760.05
111B133720.04
112J133720.04
121B134200.04
122L134200.04
131B134200.03
132N134200.03
141B132080.05
142P132080.05
151C128040.07
152E128040.07
161C127160.06
162G127160.06
171C130620.06
172I130620.06
181C128320.07
182K128320.07
191C129260.06
192M129260.06
201C127980.06
202O127980.06
211D132700.05
212F132700.05
221D132260.05
222H132260.05
231D133680.05
232J133680.05
241D133620.05
242L133620.05
251D133300.05
252N133300.05
261D131860.06
262P131860.06
271E127460.06
272G127460.06
281E128640.05
282I128640.05
291E127580.07
292K127580.07
301E129280.04
302M129280.04
311E128120.05
312O128120.05
321F133460.05
322H133460.05
331F133180.04
332J133180.04
341F133260.04
342L133260.04
351F133420.03
352N133420.03
361F133020.05
362P133020.05
371G127720.06
372I127720.06
381G127240.06
382K127240.06
391G127960.05
392M127960.05
401G128260.04
402O128260.04
411H133440.04
412J133440.04
421H133260.04
422L133260.04
431H132820.05
432N132820.05
441H133280.05
442P133280.05
451I128840.05
452K128840.05
461I129880.04
462M129880.04
471I128540.05
472O128540.05
481J134520.03
482L134520.03
491J133920.04
492N133920.04
501J132860.04
502P132860.04
511K129200.05
512M129200.05
521K128360.05
522O128360.05
531L134000.04
532N134000.04
541L133120.04
542P133120.04
551M129180.04
552O129180.04
561N132080.05
562P132080.05
571X4440.07
572Q4440.07
581X5140.15
582R5140.15
591X5020.15
592S5020.15
601X4160.09
602T4160.09
611X3740.03
612U3740.03
621X3620.13
622V3620.13
631Q4440.11
632R4440.11
641Q4400.1
642S4400.1
651Q3840.08
652T3840.08
661R5040.11
662S5040.11
671R4180.09
672T4180.09
681R3740.03
682U3740.03
691R3620.13
692V3620.13
701S4300.01
702T4300.01
711S3620.1
712U3620.1
721S3760.09
722V3760.09
731T3640.1
732U3640.1
741T3800.09
742V3800.09
751U3640.13
752V3640.13
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 325 -
Rwork0.319 6989 -
obs--99.97 %
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)
12.2118-1.7308-1.00083.4494-0.16135.25550.0211-0.20310.3568-0.02610.1122-0.60870.10760.2752-0.13330.0326-0.00370.00450.0545-0.08490.22065.7903-40.545630.7431
22.334-0.705-0.76376.7058-0.82713.28790.00160.22710.2319-0.5743-0.2936-0.82860.11630.04390.29210.29350.00630.26120.12060.08260.46595.1385-17.30938.2228
31.773-0.1209-0.10883.8871-1.65632.46330.01960.20890.2406-0.48960.0702-0.0685-0.0111-0.0726-0.08980.1299-0.03290.07030.0735-0.05770.1977-11.7795-24.237317.8278
43.9287-1.9387-0.48334.66421.63016.40510.20350.0295-0.0594-0.2084-0.11590.4394-0.3654-0.5345-0.08760.14980.027-0.02080.12810.04120.0716-78.29314.593234.2511
52.9833-1.75560.76776.88960.77824.8477-0.06940.069-0.3375-0.1169-0.02750.2712-0.0806-0.91640.09680.1466-0.03830.00330.4420.01560.0964-79.1072-17.623310.9711
63.6034-2.4755-1.85064.36122.41923.781-0.1627-0.79390.14830.45270.3837-0.26810.25250.3634-0.2210.1947-0.0434-0.09450.20910.00360.049-58.2182-5.362437.7993
71.56320.34512.00151.04960.53017.4409-0.08420.22-0.0255-0.2354-0.0149-0.1391-0.05320.02910.09910.1796-0.0206-0.02150.05310.01990.12-64.9386-17.85014.3859
84.9467-0.25510.30793.3868-1.29974.5453-0.10970.2492-0.2416-0.20650.0565-0.31320.2831-0.38960.05320.052-0.0604-0.01610.08980.03030.1086-46.6756-1.936312.3812
96.48141.3785-2.16292.1650.65775.5464-0.19490.37040.0615-0.46530.2742-0.498-0.2423-0.1175-0.07930.1791-0.04960.09310.16990.08950.3309-42.006112.0344-16.0082
104.14581.755-0.75813.3742-1.24074.00420.0115-0.21240.06580.1367-0.156-0.77220.14530.33080.14450.03360.0082-0.09370.07990.01110.3836-30.408512.590918.0693
111.65980.52171.83813.72910.39025.5146-0.29330.25840.5386-1.01920.2409-0.0836-0.9027-0.12810.05250.4963-0.07410.1010.22080.18120.5419-38.749527.7725-13.8767
125.4960.15630.84485.08791.4795.32450.07440.48980.3225-0.3753-0.06-0.1653-0.06780.4919-0.01440.05030.03430.06040.11230.05560.1354-27.9371-33.736711.0392
133.26451.955-0.34433.00942.7195.4912-0.4530.49010.6335-0.79440.63210.34980.30350.6734-0.17911.61950.1921-0.23230.3039-0.01930.7066-33.6725-49.0556-13.1377
1410.62075.73357.30036.19726.57717.33850.29540.64081.3756-0.3181-0.1994-0.24030.0597-0.1059-0.0961.4038-0.0464-0.3710.77190.37521.0016-40.1761-45.6536-22.5657
153.45931.521.29474.43180.90343.47520.5282-0.5066-0.38120.0675-0.2630.32540.3874-0.5618-0.26520.1919-0.0331-0.06730.17330.0770.2325-43.831-50.181316.0275
164.9850.0476-2.12581.08280.19824.1723-0.21860.7628-0.1982-1.15620.1716-0.20440.8980.33470.0471.72710.0778-0.03270.419-0.16640.4927-36.8032-64.7655-15.7354
175.042-1.0381-0.46672.0287-0.10111.4461-0.0195-0.0699-0.0989-0.15020.05070.30440.0324-0.2177-0.03120.1505-0.0329-0.04550.0708-0.01670.0809-13.12222.830349.7972
185.7577-0.4547-1.47352.1369-0.69512.27740.11090.32930.4443-0.03560.01790.3188-0.5242-0.3166-0.12880.28460.0045-0.05970.12350.00930.122-15.502819.397942.3595
195.6756-0.77981.36594.5490.86812.7060.10070.30830.0154-0.4599-0.013-0.4793-0.16520.157-0.08770.11350.0023-0.05770.02310.01890.412-41.206537.04098.5662
202.5191-0.79340.76287.50410.26633.41510.1780.31210.1811-0.3843-0.25110.0934-0.1374-0.00120.07310.24310.0693-0.11380.23070.04470.3518-62.592159.558-0.4412
212.7295-1.54940.52372.8242-0.80061.8843-0.0589-0.0420.30030.27440.0104-0.0213-0.1122-0.14820.04850.2335-0.04-0.09770.0377-0.03790.4021-60.571153.049219.0217
224.22411.64790.07731.73310.03571.2023-0.2210.13140.2676-0.18420.05470.2447-0.3098-0.22160.16630.47130.09030.00890.1337-0.12890.2334-86.583937.470828.659
233.28490.81870.79991.97720.14961.7087-0.0815-0.3267-0.20410.2022-0.07160.0789-0.1081-0.28940.15310.34430.06810.11520.2217-0.10070.1639-87.849521.331637.6012
243.9712.26370.23.1286-0.89781.6266-0.0045-0.687-0.43760.5484-0.0082-0.4262-0.1545-0.28950.01280.27670.1657-0.01170.3314-0.00320.33525.5842-7.45372.3443
254.07651.77510.05723.2742-0.79562.019-0.0159-0.2573-0.4389-0.08810.0903-0.21020.0286-0.1137-0.07440.10090.06240.01070.1328-0.07150.265114.8307-12.104657.8852
268.81675.0332-3.62817.67663.0777.01650.9101-1.73820.07240.9077-0.046-0.72470.01561.6907-0.8640.50840.0498-0.00540.7052-0.03990.2208-67.71621.595851.7466
276.6722-0.89550.79992.13483.22945.6331-0.0685-0.6862-0.13770.51850.1966-0.03820.82580.1428-0.12820.2872-0.0206-0.07390.36720.03860.3785-32.9447-3.422726.6636
288.05251.79173.67719.9069-9.333312.51770.4508-2.13030.57241.73360.04170.8235-1.5348-1.5254-0.49250.41150.00190.14140.6056-0.14070.261-39.9997-32.463126.8638
2911.75410.3568-10.45096.1218-2.11969.84590.29240.5408-0.8724-1.6389-1.3263-0.93790.25820.0141.03390.50810.36270.25770.8045-0.0420.30019.0257-1.280430.1718
306.34570.35151.02490.02660.05920.1845-0.10260.1145-0.3158-0.00010.0596-0.0273-0.0060.05340.0430.44190.0509-0.06880.41330.0090.58-28.489237.818922.8889
312.70772.91994.30397.5364.22336.94860.06260.1157-0.07810.0860.0069-0.6678-0.08520.2651-0.06960.5242-0.0764-0.00820.3537-0.06340.3652-64.649644.247147.1628
325.3833-4.951-2.153823.9658-10.826410.946-0.2120.38020.3194-0.44170.2215-0.3437-0.10050.3091-0.00950.3546-0.2640.00660.5834-0.01390.34443.16183.249753.3213
3311.13820.029-2.65827.0172-4.7355.78430.0471-1.1563-0.49880.4211-0.02070.38020.30820.3611-0.02640.40050.01480.010.3189-0.05030.2275-4.3303-38.159749.2875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 120
2X-RAY DIFFRACTION2A121 - 218
3X-RAY DIFFRACTION3B1 - 218
4X-RAY DIFFRACTION4C1 - 114
5X-RAY DIFFRACTION5C115 - 218
6X-RAY DIFFRACTION6D1 - 104
7X-RAY DIFFRACTION7D105 - 218
8X-RAY DIFFRACTION8E1 - 112
9X-RAY DIFFRACTION9E113 - 218
10X-RAY DIFFRACTION10F1 - 105
11X-RAY DIFFRACTION11F106 - 217
12X-RAY DIFFRACTION12G1 - 109
13X-RAY DIFFRACTION13G110 - 185
14X-RAY DIFFRACTION14G186 - 216
15X-RAY DIFFRACTION15H1 - 120
16X-RAY DIFFRACTION16H121 - 217
17X-RAY DIFFRACTION17I1 - 218
18X-RAY DIFFRACTION18J1 - 218
19X-RAY DIFFRACTION19K1 - 117
20X-RAY DIFFRACTION20K118 - 218
21X-RAY DIFFRACTION21L1 - 218
22X-RAY DIFFRACTION22M1 - 218
23X-RAY DIFFRACTION23N1 - 218
24X-RAY DIFFRACTION24O1 - 217
25X-RAY DIFFRACTION25P1 - 217
26X-RAY DIFFRACTION26Q8 - 22
27X-RAY DIFFRACTION27R9 - 23
28X-RAY DIFFRACTION28S9 - 23
29X-RAY DIFFRACTION29T11 - 23
30X-RAY DIFFRACTION30U12 - 26
31X-RAY DIFFRACTION31V12 - 23
32X-RAY DIFFRACTION32W13 - 21
33X-RAY DIFFRACTION33X9 - 23

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more