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- PDB-4oyy: Humicola insolens cutinase -

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Basic information

Entry
Database: PDB / ID: 4oyy
TitleHumicola insolens cutinase
ComponentsCutinase
KeywordsHYDROLASE
Function / homology
Function and homology information


cutinase activity / cutinase / extracellular region
Similarity search - Function
Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHumicola insolens (fungus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsDauter, Z.D. / Brzozowski, A.M. / Turkenburg, J.P. / Wilson, K.S.
CitationJournal: Protein Sci. / Year: 2014
Title: Thermodynamic and structural investigation of the specific SDS binding of humicola insolens cutinase.
Authors: Kold, D. / Dauter, Z. / Laustsen, A.K. / Brzozowski, A.M. / Turkenburg, J.P. / Nielsen, A.D. / Kolds, H. / Petersen, E. / Schitt, B. / De Maria, L. / Wilson, K.S. / Svendsen, A. / Wimmer, R.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Data collection / Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Cutinase
B: Cutinase
C: Cutinase
D: Cutinase
E: Cutinase
F: Cutinase
G: Cutinase
H: Cutinase
I: Cutinase
J: Cutinase
K: Cutinase
L: Cutinase


Theoretical massNumber of molelcules
Total (without water)243,25112
Polymers243,25112
Non-polymers00
Water1,76598
1
A: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,2711
Polymers20,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.548, 126.999, 134.505
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
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

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
11GLYGLYARGARGAA3 - 1933 - 193
21GLYGLYARGARGBB3 - 1933 - 193
12GLYGLYILEILEAA3 - 1923 - 192
22GLYGLYILEILECC3 - 1923 - 192
13GLYGLYARGARGAA3 - 1933 - 193
23GLYGLYARGARGDD3 - 1933 - 193
14GLYGLYARGARGAA3 - 1933 - 193
24GLYGLYARGARGEE3 - 1933 - 193
15GLYGLYILEILEAA3 - 1923 - 192
25GLYGLYILEILEFF3 - 1923 - 192
16GLYGLYILEILEAA3 - 1923 - 192
26GLYGLYILEILEGG3 - 1923 - 192
17GLYGLYARGARGAA3 - 1933 - 193
27GLYGLYARGARGHH3 - 1933 - 193
18GLYGLYILEILEAA3 - 1923 - 192
28GLYGLYILEILEII3 - 1923 - 192
19GLYGLYARGARGAA3 - 1933 - 193
29GLYGLYARGARGJJ3 - 1933 - 193
110GLYGLYARGARGAA3 - 1933 - 193
210GLYGLYARGARGKK3 - 1933 - 193
111GLYGLYILEILEAA3 - 1923 - 192
211GLYGLYILEILELL3 - 1923 - 192
112GLYGLYILEILEBB3 - 1923 - 192
212GLYGLYILEILECC3 - 1923 - 192
113GLYGLYARGARGBB3 - 1933 - 193
213GLYGLYARGARGDD3 - 1933 - 193
114GLYGLYARGARGBB3 - 1933 - 193
214GLYGLYARGARGEE3 - 1933 - 193
115GLYGLYILEILEBB3 - 1923 - 192
215GLYGLYILEILEFF3 - 1923 - 192
116GLYGLYILEILEBB3 - 1923 - 192
216GLYGLYILEILEGG3 - 1923 - 192
117GLYGLYARGARGBB3 - 1933 - 193
217GLYGLYARGARGHH3 - 1933 - 193
118GLYGLYILEILEBB3 - 1923 - 192
218GLYGLYILEILEII3 - 1923 - 192
119GLYGLYARGARGBB3 - 1933 - 193
219GLYGLYARGARGJJ3 - 1933 - 193
120GLYGLYARGARGBB3 - 1933 - 193
220GLYGLYARGARGKK3 - 1933 - 193
121GLYGLYILEILEBB3 - 1923 - 192
221GLYGLYILEILELL3 - 1923 - 192
122GLYGLYILEILECC3 - 1923 - 192
222GLYGLYILEILEDD3 - 1923 - 192
123GLYGLYILEILECC3 - 1923 - 192
223GLYGLYILEILEEE3 - 1923 - 192
124GLNGLNARGARGCC1 - 1931 - 193
224GLNGLNARGARGFF1 - 1931 - 193
125GLNGLNARGARGCC1 - 1931 - 193
225GLNGLNARGARGGG1 - 1931 - 193
126GLYGLYILEILECC3 - 1923 - 192
226GLYGLYILEILEHH3 - 1923 - 192
127GLNGLNARGARGCC1 - 1931 - 193
227GLNGLNARGARGII1 - 1931 - 193
128GLYGLYILEILECC3 - 1923 - 192
228GLYGLYILEILEJJ3 - 1923 - 192
129GLYGLYILEILECC3 - 1923 - 192
229GLYGLYILEILEKK3 - 1923 - 192
130LEULEUILEILECC2 - 1922 - 192
230LEULEUILEILELL2 - 1922 - 192
131GLYGLYARGARGDD3 - 1933 - 193
231GLYGLYARGARGEE3 - 1933 - 193
132GLYGLYILEILEDD3 - 1923 - 192
232GLYGLYILEILEFF3 - 1923 - 192
133GLYGLYILEILEDD3 - 1923 - 192
233GLYGLYILEILEGG3 - 1923 - 192
134GLYGLYARGARGDD3 - 1933 - 193
234GLYGLYARGARGHH3 - 1933 - 193
135GLYGLYILEILEDD3 - 1923 - 192
235GLYGLYILEILEII3 - 1923 - 192
136GLYGLYARGARGDD3 - 1933 - 193
236GLYGLYARGARGJJ3 - 1933 - 193
137GLYGLYARGARGDD3 - 1933 - 193
237GLYGLYARGARGKK3 - 1933 - 193
138GLYGLYILEILEDD3 - 1923 - 192
238GLYGLYILEILELL3 - 1923 - 192
139GLYGLYILEILEEE3 - 1923 - 192
239GLYGLYILEILEFF3 - 1923 - 192
140GLYGLYILEILEEE3 - 1923 - 192
240GLYGLYILEILEGG3 - 1923 - 192
141GLYGLYARGARGEE3 - 1933 - 193
241GLYGLYARGARGHH3 - 1933 - 193
142GLYGLYILEILEEE3 - 1923 - 192
242GLYGLYILEILEII3 - 1923 - 192
143GLYGLYARGARGEE3 - 1933 - 193
243GLYGLYARGARGJJ3 - 1933 - 193
144GLYGLYARGARGEE3 - 1933 - 193
244GLYGLYARGARGKK3 - 1933 - 193
145GLYGLYILEILEEE3 - 1923 - 192
245GLYGLYILEILELL3 - 1923 - 192
146GLNGLNARGARGFF1 - 1931 - 193
246GLNGLNARGARGGG1 - 1931 - 193
147GLYGLYILEILEFF3 - 1923 - 192
247GLYGLYILEILEHH3 - 1923 - 192
148GLNGLNARGARGFF1 - 1931 - 193
248GLNGLNARGARGII1 - 1931 - 193
149GLYGLYILEILEFF3 - 1923 - 192
249GLYGLYILEILEJJ3 - 1923 - 192
150GLYGLYILEILEFF3 - 1923 - 192
250GLYGLYILEILEKK3 - 1923 - 192
151LEULEUILEILEFF2 - 1922 - 192
251LEULEUILEILELL2 - 1922 - 192
152GLYGLYILEILEGG3 - 1923 - 192
252GLYGLYILEILEHH3 - 1923 - 192
153GLNGLNARGARGGG1 - 1931 - 193
253GLNGLNARGARGII1 - 1931 - 193
154GLYGLYILEILEGG3 - 1923 - 192
254GLYGLYILEILEJJ3 - 1923 - 192
155GLYGLYILEILEGG3 - 1923 - 192
255GLYGLYILEILEKK3 - 1923 - 192
156LEULEUILEILEGG2 - 1922 - 192
256LEULEUILEILELL2 - 1922 - 192
157GLYGLYILEILEHH3 - 1923 - 192
257GLYGLYILEILEII3 - 1923 - 192
158GLYGLYARGARGHH3 - 1933 - 193
258GLYGLYARGARGJJ3 - 1933 - 193
159GLYGLYARGARGHH3 - 1933 - 193
259GLYGLYARGARGKK3 - 1933 - 193
160GLYGLYILEILEHH3 - 1923 - 192
260GLYGLYILEILELL3 - 1923 - 192
161GLYGLYILEILEII3 - 1923 - 192
261GLYGLYILEILEJJ3 - 1923 - 192
162GLYGLYILEILEII3 - 1923 - 192
262GLYGLYILEILEKK3 - 1923 - 192
163LEULEUILEILEII2 - 1922 - 192
263LEULEUILEILELL2 - 1922 - 192
164GLYGLYARGARGJJ3 - 1933 - 193
264GLYGLYARGARGKK3 - 1933 - 193
165GLYGLYILEILEJJ3 - 1923 - 192
265GLYGLYILEILELL3 - 1923 - 192
166GLYGLYILEILEKK3 - 1923 - 192
266GLYGLYILEILELL3 - 1923 - 192

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

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Components

#1: Protein
Cutinase


Mass: 20270.889 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humicola insolens (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A075B5G4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: HiCutinase 30 mg mL-1, 0.1 M Tris/HCl buffer pH 8.5, 50 mM lysine, 100 mg mL-1 (app. 8.6%) isopropanol, 50 mg mL-1 (app. 4.3 %) dioxane, PEG 4K 22% v/v of 50% w/v stock solutions

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 20, 1995
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 43738 / % possible obs: 99.5 % / Redundancy: 4.5 % / Net I/σ(I): 5.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
AMoREphasing
REFMAC5.8.0049refinement
RefinementResolution: 3→29.7611 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.957 / SU B: 15.789 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19597 1338 3.1 %RANDOM
Rwork0.1741 ---
obs0.17481 42118 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.819 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å2-0 Å2
2--2.39 Å2-0 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 3→29.7611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16877 0 0 98 16975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01917189
X-RAY DIFFRACTIONr_bond_other_d0.0080.0216543
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.95923355
X-RAY DIFFRACTIONr_angle_other_deg1.539337829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62452289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08323.844731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.371152624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.25815141
X-RAY DIFFRACTIONr_chiral_restr0.0840.22630
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120270
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023987
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_it1.7572.6179192
X-RAY DIFFRACTIONr_mcbond_other1.7562.6179191
X-RAY DIFFRACTIONr_mcangle_it2.9173.92411469
X-RAY DIFFRACTIONr_mcangle_other2.9183.92411470
X-RAY DIFFRACTIONr_scbond_it2.3122.9257997
X-RAY DIFFRACTIONr_scbond_other2.3122.9267998
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8694.27111887
X-RAY DIFFRACTIONr_long_range_B_refined5.3920.77118530
X-RAY DIFFRACTIONr_long_range_B_other5.3920.77318531
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)
11A112290.07
12B112290.07
21A110320.07
22C110320.07
31A114570.05
32D114570.05
41A110740.07
42E110740.07
51A110690.07
52F110690.07
61A112340.06
62G112340.06
71A113370.06
72H113370.06
81A110510.06
82I110510.06
91A113800.06
92J113800.06
101A112440.06
102K112440.06
111A110350.08
112L110350.08
121B109060.08
122C109060.08
131B112280.07
132D112280.07
141B111030.08
142E111030.08
151B109530.08
152F109530.08
161B110150.08
162G110150.08
171B113580.06
172H113580.06
181B108920.07
182I108920.07
191B111440.08
192J111440.08
201B112760.06
202K112760.06
211B109380.09
212L109380.09
221C110180.07
222D110180.07
231C108640.08
232E108640.08
241C113920.06
242F113920.06
251C112370.07
252G112370.07
261C109550.08
262H109550.08
271C111800.07
272I111800.07
281C110390.07
282J110390.07
291C110050.07
292K110050.07
301C111650.08
302L111650.08
311D110630.07
312E110630.07
321D110860.06
322F110860.06
331D111980.06
332G111980.06
341D112940.06
342H112940.06
351D110350.06
352I110350.06
361D113370.07
362J113370.07
371D112350.06
372K112350.06
381D110170.08
382L110170.08
391E108600.08
392F108600.08
401E109440.07
402G109440.07
411E111140.07
412H111140.07
421E107820.08
422I107820.08
431E110630.07
432J110630.07
441E111060.07
442K111060.07
451E108720.09
452L108720.09
461F112330.07
462G112330.07
471F110040.08
472H110040.08
481F112860.06
482I112860.06
491F110390.07
492J110390.07
501F110250.07
502K110250.07
511F111880.08
512L111880.08
521G110940.07
522H110940.07
531G111770.07
532I111770.07
541G112100.05
542J112100.05
551G110650.06
552K110650.06
561G111070.08
562L111070.08
571H109450.07
572I109450.07
581H112610.07
582J112610.07
591H113500.05
592K113500.05
601H109710.09
602L109710.09
611I109540.07
612J109540.07
621I111210.05
622K111210.05
631I110420.08
632L110420.08
641J111960.07
642K111960.07
651J111010.07
652L111010.07
661K110320.08
662L110320.08
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 96 -
Rwork0.262 3010 -
obs--97.31 %

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