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- PDB-7ag7: Crystal structure of SFP aldolase YihT from Salmonella enterica i... -

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Basic information

Entry
Database: PDB / ID: 7ag7
TitleCrystal structure of SFP aldolase YihT from Salmonella enterica in complex with sulfate bound at the active site
ComponentsSulfofructosephosphate aldolase
KeywordsLYASE / sulfofructose / sulfoquinovose / SFP aldolase / sulfoglycolysis
Function / homology
Function and homology information


sulfofructosephosphate aldolase / 6-deoxy-6-sulfofructose-1-phosphate aldolase activity / 6-sulfoquinovose(1-) catabolic process / carbohydrate metabolic process
Similarity search - Function
Sulfofructosephosphate aldolase, YihT / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Sulfofructosephosphate aldolase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-190 United Kingdom
CitationJournal: Acs Cent.Sci. / Year: 2021
Title: Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis.
Authors: Sharma, M. / Abayakoon, P. / Epa, R. / Jin, Y. / Lingford, J.P. / Shimada, T. / Nakano, M. / Mui, J.W. / Ishihama, A. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
History
DepositionSep 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Sulfofructosephosphate aldolase
B: Sulfofructosephosphate aldolase
C: Sulfofructosephosphate aldolase
D: Sulfofructosephosphate aldolase
E: Sulfofructosephosphate aldolase
F: Sulfofructosephosphate aldolase
G: Sulfofructosephosphate aldolase
H: Sulfofructosephosphate aldolase
I: Sulfofructosephosphate aldolase
J: Sulfofructosephosphate aldolase
K: Sulfofructosephosphate aldolase
L: Sulfofructosephosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,06824
Polymers408,91512
Non-polymers1,15312
Water33,6881870
1
B: Sulfofructosephosphate aldolase
J: Sulfofructosephosphate aldolase
hetero molecules

A: Sulfofructosephosphate aldolase
C: Sulfofructosephosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6898
Polymers136,3054
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
2
D: Sulfofructosephosphate aldolase
I: Sulfofructosephosphate aldolase
hetero molecules

K: Sulfofructosephosphate aldolase
L: Sulfofructosephosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6898
Polymers136,3054
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
3
E: Sulfofructosephosphate aldolase
G: Sulfofructosephosphate aldolase
hetero molecules

F: Sulfofructosephosphate aldolase
hetero molecules

H: Sulfofructosephosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6898
Polymers136,3054
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_454x-1,y,z-11
Unit cell
Length a, b, c (Å)85.207, 107.233, 126.855
Angle α, β, γ (deg.)107.420, 95.930, 110.550
Int Tables number1
Space group name H-MP1
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: 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
11TYRTYRLYSLYSAA4 - 29024 - 310
21TYRTYRLYSLYSBB4 - 29024 - 310
12TYRTYRLYSLYSAA4 - 29024 - 310
22TYRTYRLYSLYSCC4 - 29024 - 310
13TYRTYRARGARGAA4 - 29124 - 311
23TYRTYRARGARGDD4 - 29124 - 311
14TYRTYRLYSLYSAA4 - 29024 - 310
24TYRTYRLYSLYSEE4 - 29024 - 310
15THRTHRLYSLYSAA10 - 29030 - 310
25THRTHRLYSLYSFF10 - 29030 - 310
16TYRTYRALAALAAA4 - 28924 - 309
26TYRTYRALAALAGG4 - 28924 - 309
17THRTHRLYSLYSAA5 - 29025 - 310
27THRTHRLYSLYSHH5 - 29025 - 310
18TYRTYRLYSLYSAA4 - 29024 - 310
28TYRTYRLYSLYSII4 - 29024 - 310
19TYRTYRLYSLYSAA4 - 29024 - 310
29TYRTYRLYSLYSJJ4 - 29024 - 310
110TYRTYRLYSLYSAA4 - 29024 - 310
210TYRTYRLYSLYSKK4 - 29024 - 310
111TYRTYRLYSLYSAA4 - 29024 - 310
211TYRTYRLYSLYSLL4 - 29024 - 310
112ASNASNLYSLYSBB2 - 29022 - 310
212ASNASNLYSLYSCC2 - 29022 - 310
113METMETLYSLYSBB1 - 29021 - 310
213METMETLYSLYSDD1 - 29021 - 310
114METMETLYSLYSBB1 - 29021 - 310
214METMETLYSLYSEE1 - 29021 - 310
115THRTHRLYSLYSBB10 - 29030 - 310
215THRTHRLYSLYSFF10 - 29030 - 310
116ASNASNALAALABB3 - 28923 - 309
216ASNASNALAALAGG3 - 28923 - 309
117THRTHRLYSLYSBB5 - 29025 - 310
217THRTHRLYSLYSHH5 - 29025 - 310
118ASNASNLYSLYSBB3 - 29023 - 310
218ASNASNLYSLYSII3 - 29023 - 310
119ASNASNLYSLYSBB3 - 29023 - 310
219ASNASNLYSLYSJJ3 - 29023 - 310
120ASNASNLYSLYSBB3 - 29023 - 310
220ASNASNLYSLYSKK3 - 29023 - 310
121ASNASNLYSLYSBB3 - 29023 - 310
221ASNASNLYSLYSLL3 - 29023 - 310
122ASNASNLYSLYSCC2 - 29022 - 310
222ASNASNLYSLYSDD2 - 29022 - 310
123ASNASNLYSLYSCC2 - 29022 - 310
223ASNASNLYSLYSEE2 - 29022 - 310
124THRTHRLYSLYSCC10 - 29030 - 310
224THRTHRLYSLYSFF10 - 29030 - 310
125ASNASNALAALACC3 - 28923 - 309
225ASNASNALAALAGG3 - 28923 - 309
126THRTHRLYSLYSCC5 - 29025 - 310
226THRTHRLYSLYSHH5 - 29025 - 310
127ASNASNLYSLYSCC3 - 29023 - 310
227ASNASNLYSLYSII3 - 29023 - 310
128ASNASNLYSLYSCC3 - 29023 - 310
228ASNASNLYSLYSJJ3 - 29023 - 310
129ASNASNLYSLYSCC3 - 29023 - 310
229ASNASNLYSLYSKK3 - 29023 - 310
130ASNASNLYSLYSCC3 - 29023 - 310
230ASNASNLYSLYSLL3 - 29023 - 310
131HISHISLYSLYSDD0 - 29020 - 310
231HISHISLYSLYSEE0 - 29020 - 310
132THRTHRLYSLYSDD10 - 29030 - 310
232THRTHRLYSLYSFF10 - 29030 - 310
133ASNASNALAALADD3 - 28923 - 309
233ASNASNALAALAGG3 - 28923 - 309
134THRTHRLYSLYSDD5 - 29025 - 310
234THRTHRLYSLYSHH5 - 29025 - 310
135ASNASNLYSLYSDD3 - 29023 - 310
235ASNASNLYSLYSII3 - 29023 - 310
136ASNASNLYSLYSDD3 - 29023 - 310
236ASNASNLYSLYSJJ3 - 29023 - 310
137ASNASNLYSLYSDD3 - 29023 - 310
237ASNASNLYSLYSKK3 - 29023 - 310
138ASNASNLYSLYSDD3 - 29023 - 310
238ASNASNLYSLYSLL3 - 29023 - 310
139THRTHRLYSLYSEE10 - 29030 - 310
239THRTHRLYSLYSFF10 - 29030 - 310
140ASNASNALAALAEE3 - 28923 - 309
240ASNASNALAALAGG3 - 28923 - 309
141THRTHRLYSLYSEE5 - 29025 - 310
241THRTHRLYSLYSHH5 - 29025 - 310
142ASNASNLYSLYSEE3 - 29023 - 310
242ASNASNLYSLYSII3 - 29023 - 310
143ASNASNLYSLYSEE3 - 29023 - 310
243ASNASNLYSLYSJJ3 - 29023 - 310
144ASNASNLYSLYSEE3 - 29023 - 310
244ASNASNLYSLYSKK3 - 29023 - 310
145ASNASNLYSLYSEE3 - 29023 - 310
245ASNASNLYSLYSLL3 - 29023 - 310
146THRTHRALAALAFF10 - 28930 - 309
246THRTHRALAALAGG10 - 28930 - 309
147THRTHRARGARGFF10 - 29130 - 311
247THRTHRARGARGHH10 - 29130 - 311
148THRTHRLYSLYSFF10 - 29030 - 310
248THRTHRLYSLYSII10 - 29030 - 310
149THRTHRLYSLYSFF10 - 29030 - 310
249THRTHRLYSLYSJJ10 - 29030 - 310
150THRTHRLYSLYSFF10 - 29030 - 310
250THRTHRLYSLYSKK10 - 29030 - 310
151THRTHRLYSLYSFF10 - 29030 - 310
251THRTHRLYSLYSLL10 - 29030 - 310
152THRTHRALAALAGG5 - 28925 - 309
252THRTHRALAALAHH5 - 28925 - 309
153ASNASNALAALAGG3 - 28923 - 309
253ASNASNALAALAII3 - 28923 - 309
154ASNASNALAALAGG3 - 28923 - 309
254ASNASNALAALAJJ3 - 28923 - 309
155ASNASNALAALAGG3 - 28923 - 309
255ASNASNALAALAKK3 - 28923 - 309
156ASNASNALAALAGG3 - 28923 - 309
256ASNASNALAALALL3 - 28923 - 309
157THRTHRLYSLYSHH5 - 29025 - 310
257THRTHRLYSLYSII5 - 29025 - 310
158THRTHRLYSLYSHH5 - 29025 - 310
258THRTHRLYSLYSJJ5 - 29025 - 310
159THRTHRLYSLYSHH5 - 29025 - 310
259THRTHRLYSLYSKK5 - 29025 - 310
160THRTHRLYSLYSHH5 - 29025 - 310
260THRTHRLYSLYSLL5 - 29025 - 310
161ASNASNARGARGII3 - 29123 - 311
261ASNASNARGARGJJ3 - 29123 - 311
162ASNASNARGARGII3 - 29123 - 311
262ASNASNARGARGKK3 - 29123 - 311
163ASNASNARGARGII3 - 29123 - 311
263ASNASNARGARGLL3 - 29123 - 311
164ASNASNARGARGJJ3 - 29123 - 311
264ASNASNARGARGKK3 - 29123 - 311
165ASNASNARGARGJJ3 - 29123 - 311
265ASNASNARGARGLL3 - 29123 - 311
166ASNASNARGARGKK3 - 29123 - 311
266ASNASNARGARGLL3 - 29123 - 311

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
Sulfofructosephosphate aldolase / SFP aldolase


Mass: 34076.262 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: yihT, STM4022 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9L7R9, sulfofructosephosphate aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1870 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.44 Å3/Da / Density % sol: 64.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2 M Na2SO4, 0.1M BisTris propane pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→53.71 Å / Num. obs: 352557 / % possible obs: 97.5 % / Redundancy: 2.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.034 / Rrim(I) all: 0.055 / Net I/σ(I): 9.2 / Num. measured all: 786014 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.832.10.32436708172220.8410.2720.4252.396.1
9.86-53.712.20.024477921710.9980.0190.03119.498.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TO3
Resolution: 1.8→53.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.592 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 17503 5 %RANDOM
Rwork0.193 ---
obs0.1937 335012 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.65 Å2 / Biso mean: 26.46 Å2 / Biso min: 11.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0.32 Å2-0.46 Å2
2--1.09 Å2-0.11 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.8→53.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25659 0 60 1870 27589
Biso mean--25.01 29.25 -
Num. residues----3461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01326155
X-RAY DIFFRACTIONr_bond_other_d0.0010.01725227
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.62735488
X-RAY DIFFRACTIONr_angle_other_deg1.4661.5857768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37153477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16921.9711253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.847154328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.41715196
X-RAY DIFFRACTIONr_chiral_restr0.0780.23482
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0230258
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025774
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89760.06
12B89760.06
21A91170.05
22C91170.05
31A90980.06
32D90980.06
41A89950.06
42E89950.06
51A78360.05
52F78360.05
61A89870.07
62G89870.07
71A89060.06
72H89060.06
81A91000.06
82I91000.06
91A90380.05
92J90380.05
101A91070.05
102K91070.05
111A90940.06
112L90940.06
121B90040.06
122C90040.06
131B91270.05
132D91270.05
141B90900.04
142E90900.04
151B77930.05
152F77930.05
161B89800.06
162G89800.06
171B88650.05
172H88650.05
181B90570.04
182I90570.04
191B90400.04
192J90400.04
201B90040.06
202K90040.06
211B89780.05
212L89780.05
221C90880.06
222D90880.06
231C90360.06
232E90360.06
241C78050.05
242F78050.05
251C89710.07
252G89710.07
261C88910.05
262H88910.05
271C91020.05
272I91020.05
281C90140.06
282J90140.06
291C91660.05
292K91660.05
301C91090.05
302L91090.05
311D92600.04
312E92600.04
321D78010.06
322F78010.06
331D90730.06
332G90730.06
341D89160.05
342H89160.05
351D91550.05
352I91550.05
361D91210.05
362J91210.05
371D91300.07
372K91300.07
381D90830.06
382L90830.06
391E78040.05
392F78040.05
401E90090.06
402G90090.06
411E88990.04
412H88990.04
421E90910.04
422I90910.04
431E90580.04
432J90580.04
441E90490.06
442K90490.06
451E90220.05
452L90220.05
461F77720.06
462G77720.06
471F78020.05
472H78020.05
481F78290.04
482I78290.04
491F78400.04
492J78400.04
501F78180.04
502K78180.04
511F78190.05
512L78190.05
521G89290.05
522H89290.05
531G91170.06
532I91170.06
541G90770.06
542J90770.06
551G90450.07
552K90450.07
561G90160.07
562L90160.07
571H89190.04
572I89190.04
581H89060.04
582J89060.04
591H89220.05
592K89220.05
601H88910.05
602L88910.05
611I91580.05
612J91580.05
621I91740.06
622K91740.06
631I91490.05
632L91490.05
641J90950.06
642K90950.06
651J90760.06
652L90760.06
661K91160.06
662L91160.06
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 1279 -
Rwork0.258 24499 -
all-25778 -
obs--96.03 %

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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

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