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- PDB-6i9g: Crystal structure of encapsulin from Mycolicibacterium hassiacum -

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Basic information

Entry
Database: PDB / ID: 6i9g
TitleCrystal structure of encapsulin from Mycolicibacterium hassiacum
ComponentsLinocin-M18
KeywordsVIRUS LIKE PARTICLE / Nanocompartment / nanocage / packaging of biocatalysts / bacteriocin
Function / homology
Function and homology information


encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / hydrolase activity
Similarity search - Function
Major capsid protein gp5 fold - #30 / Major capsid protein gp5 fold / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycolicibacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structure of a robust bacterial protein cage and its application as a versatile biocatalytic platform through enzyme encapsulation.
Authors: Loncar, N. / Rozeboom, H.J. / Franken, L.E. / Stuart, M.C.A. / Fraaije, M.W.
History
DepositionNov 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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
A: Linocin-M18
B: Linocin-M18
C: Linocin-M18
D: Linocin-M18
E: Linocin-M18
F: Linocin-M18
G: Linocin-M18
H: Linocin-M18
I: Linocin-M18
J: Linocin-M18
K: Linocin-M18
L: Linocin-M18
M: Linocin-M18
N: Linocin-M18
O: Linocin-M18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,810136
Polymers435,20215
Non-polymers11,608121
Water50,3882797
1
A: Linocin-M18
B: Linocin-M18
C: Linocin-M18
D: Linocin-M18
E: Linocin-M18
F: Linocin-M18
G: Linocin-M18
H: Linocin-M18
I: Linocin-M18
J: Linocin-M18
K: Linocin-M18
L: Linocin-M18
M: Linocin-M18
N: Linocin-M18
O: Linocin-M18
hetero molecules

A: Linocin-M18
B: Linocin-M18
C: Linocin-M18
D: Linocin-M18
E: Linocin-M18
F: Linocin-M18
G: Linocin-M18
H: Linocin-M18
I: Linocin-M18
J: Linocin-M18
K: Linocin-M18
L: Linocin-M18
M: Linocin-M18
N: Linocin-M18
O: Linocin-M18
hetero molecules

A: Linocin-M18
B: Linocin-M18
C: Linocin-M18
D: Linocin-M18
E: Linocin-M18
F: Linocin-M18
G: Linocin-M18
H: Linocin-M18
I: Linocin-M18
J: Linocin-M18
K: Linocin-M18
L: Linocin-M18
M: Linocin-M18
N: Linocin-M18
O: Linocin-M18
hetero molecules

A: Linocin-M18
B: Linocin-M18
C: Linocin-M18
D: Linocin-M18
E: Linocin-M18
F: Linocin-M18
G: Linocin-M18
H: Linocin-M18
I: Linocin-M18
J: Linocin-M18
K: Linocin-M18
L: Linocin-M18
M: Linocin-M18
N: Linocin-M18
O: Linocin-M18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,787,239544
Polymers1,740,80860
Non-polymers46,431484
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area298320 Å2
ΔGint-587 kcal/mol
Surface area523010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.272, 242.149, 271.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11D-558-

HOH

21K-536-

HOH

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
112A
212M
113A
213N
114A
214O
115B
215C
116B
216D
117B
217E
118B
218F
119B
219G
120B
220H
121B
221I
122B
222J
123B
223K
124B
224L
125B
225M
126B
226N
127B
227O
128C
228D
129C
229E
130C
230F
131C
231G
132C
232H
133C
233I
134C
234J
135C
235K
136C
236L
137C
237M
138C
238N
139C
239O
140D
240E
141D
241F
142D
242G
143D
243H
144D
244I
145D
245J
146D
246K
147D
247L
148D
248M
149D
249N
150D
250O
151E
251F
152E
252G
153E
253H
154E
254I
155E
255J
156E
256K
157E
257L
158E
258M
159E
259N
160E
260O
161F
261G
162F
262H
163F
263I
164F
264J
165F
265K
166F
266L
167F
267M
168F
268N
169F
269O
170G
270H
171G
271I
172G
272J
173G
273K
174G
274L
175G
275M
176G
276N
177G
277O
178H
278I
179H
279J
180H
280K
181H
281L
182H
282M
183H
283N
184H
284O
185I
285J
186I
286K
187I
287L
188I
288M
189I
289N
190I
290O
191J
291K
192J
292L
193J
293M
194J
294N
195J
295O
196K
296L
197K
297M
198K
298N
199K
299O
1100L
2100M
1101L
2101N
1102L
2102O
1103M
2103N
1104M
2104O
1105N
2105O

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 1 - 265 / Label seq-ID: 1 - 265

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18AA
28II
19AA
29JJ
110AA
210KK
111AA
211LL
112AA
212MM
113AA
213NN
114AA
214OO
115BB
215CC
116BB
216DD
117BB
217EE
118BB
218FF
119BB
219GG
120BB
220HH
121BB
221II
122BB
222JJ
123BB
223KK
124BB
224LL
125BB
225MM
126BB
226NN
127BB
227OO
128CC
228DD
129CC
229EE
130CC
230FF
131CC
231GG
132CC
232HH
133CC
233II
134CC
234JJ
135CC
235KK
136CC
236LL
137CC
237MM
138CC
238NN
139CC
239OO
140DD
240EE
141DD
241FF
142DD
242GG
143DD
243HH
144DD
244II
145DD
245JJ
146DD
246KK
147DD
247LL
148DD
248MM
149DD
249NN
150DD
250OO
151EE
251FF
152EE
252GG
153EE
253HH
154EE
254II
155EE
255JJ
156EE
256KK
157EE
257LL
158EE
258MM
159EE
259NN
160EE
260OO
161FF
261GG
162FF
262HH
163FF
263II
164FF
264JJ
165FF
265KK
166FF
266LL
167FF
267MM
168FF
268NN
169FF
269OO
170GG
270HH
171GG
271II
172GG
272JJ
173GG
273KK
174GG
274LL
175GG
275MM
176GG
276NN
177GG
277OO
178HH
278II
179HH
279JJ
180HH
280KK
181HH
281LL
182HH
282MM
183HH
283NN
184HH
284OO
185II
285JJ
186II
286KK
187II
287LL
188II
288MM
189II
289NN
190II
290OO
191JJ
291KK
192JJ
292LL
193JJ
293MM
194JJ
294NN
195JJ
295OO
196KK
296LL
197KK
297MM
198KK
298NN
199KK
299OO
1100LL
2100MM
1101LL
2101NN
1102LL
2102OO
1103MM
2103NN
1104MM
2104OO
1105NN
2105OO

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

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Components

#1: Protein
Linocin-M18


Mass: 29013.471 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium hassiacum DSM 44199 (bacteria)
Gene: lin, C731_3737 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB 10 beta
References: UniProt: K5BEG2, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 117 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2797 / 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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 6.0 mg/ml encapsulin. 1.3 -1.6 M ammonium sulfate, 0.1 MES buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→47.8 Å / Num. obs: 255440 / % possible obs: 98.2 % / Redundancy: 3.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.084 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 12672 / CC1/2: 0.497 / Rpim(I) all: 0.365 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DKT
Resolution: 2.5→47.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.576 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.202 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21048 12567 4.9 %RANDOM
Rwork0.17236 ---
obs0.17422 242842 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 28.932 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å2-0 Å2
2--0.41 Å20 Å2
3----1.46 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30675 0 609 2798 34082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01931808
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.98143487
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68853960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91823.3681425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.935154920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.97215285
X-RAY DIFFRACTIONr_chiral_restr0.080.25101
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02124000
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4562.57815885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3133.86319830
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4463.06415923
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.0722.81350558
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A360
12B360
21A364
22C364
31A364
32D364
41A360
42E360
51A362
52F362
61A365
62G365
71A361
72H361
81A357
82I357
91A361
92J361
101A360
102K360
111A363
112L363
121A362
122M362
131A361
132N361
141A360
142O360
151B360
152C360
161B364
162D364
171B360
172E360
181B363
182F363
191B360
192G360
201B359
202H359
211B357
212I357
221B360
222J360
231B360
232K360
241B361
242L361
251B361
252M361
261B360
262N360
271B357
272O357
281C365
282D365
291C361
292E361
301C362
302F362
311C363
312G363
321C360
322H360
331C360
332I360
341C362
342J362
351C361
352K361
361C363
362L363
371C362
372M362
381C364
382N364
391C359
392O359
401D365
402E365
411D366
412F366
421D363
422G363
431D361
432H361
441D362
442I362
451D363
452J363
461D363
462K363
471D366
472L366
481D364
482M364
491D362
492N362
501D361
502O361
511E361
512F361
521E362
522G362
531E356
532H356
541E360
542I360
551E360
552J360
561E363
562K363
571E362
572L362
581E364
582M364
591E361
592N361
601E359
602O359
611F362
612G362
621F361
622H361
631F360
632I360
641F361
642J361
651F362
652K362
661F362
662L362
671F362
672M362
681F362
682N362
691F359
692O359
701G360
702H360
711G360
712I360
721G362
722J362
731G362
732K362
741G362
742L362
751G364
752M364
761G364
762N364
771G358
772O358
781H355
782I355
791H361
792J361
801H357
802K357
811H358
812L358
821H359
822M359
831H360
832N360
841H357
842O357
851I361
852J361
861I362
862K362
871I364
872L364
881I362
882M362
891I362
892N362
901I360
902O360
911J364
912K364
921J365
922L365
931J366
932M366
941J365
942N365
951J361
952O361
961K365
962L365
971K365
972M365
981K363
982N363
991K363
992O363
1001L365
1002M365
1011L363
1012N363
1021L363
1022O363
1031M365
1032N365
1041M362
1042O362
1051N362
1052O362
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 966 -
Rwork0.279 17978 -
obs--98.85 %

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