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- PDB-2qq2: Crystal structure of C-terminal domain of Human acyl-CoA thioeste... -

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Basic information

Entry
Database: PDB / ID: 2qq2
TitleCrystal structure of C-terminal domain of Human acyl-CoA thioesterase 7
ComponentsCytosolic acyl coenzyme A thioester hydrolase
KeywordsHYDROLASE / Acot7 / C-terminal domain / thioesterase / Structural Genomics / Structural Genomics Consortium / SGC / Hydrolase / Mitochondrion / Serine esterase
Function / homology
Function and homology information


Mitochondrial Fatty Acid Beta-Oxidation / medium-chain fatty-acyl-CoA catabolic process / long-chain fatty-acyl-CoA catabolic process / medium-chain fatty acid biosynthetic process / palmitic acid biosynthetic process / long-chain fatty acyl-CoA binding / myristoyl-CoA hydrolase activity / palmitoyl-CoA hydrolase / palmitoyl-CoA hydrolase activity / acyl-CoA hydrolase activity ...Mitochondrial Fatty Acid Beta-Oxidation / medium-chain fatty-acyl-CoA catabolic process / long-chain fatty-acyl-CoA catabolic process / medium-chain fatty acid biosynthetic process / palmitic acid biosynthetic process / long-chain fatty acyl-CoA binding / myristoyl-CoA hydrolase activity / palmitoyl-CoA hydrolase / palmitoyl-CoA hydrolase activity / acyl-CoA hydrolase activity / acyl-CoA metabolic process / fatty-acyl-CoA binding / carboxylic ester hydrolase activity / coenzyme A biosynthetic process / protein homodimerization activity / mitochondrion / extracellular exosome / nucleoplasm / cytosol
Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Thioesterase superfamily / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain / HotDog domain superfamily / Thioesterase domain
Cytosolic acyl coenzyme A thioester hydrolase
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBusam, R. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Herman, M.D. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Welin, M. / Persson, C. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human acyl-CoA thioesterase 7.
Authors: Busam, R. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Herman, M.D. / Edwards, A. / Flodin, S. / Flores, A. / Greslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Welin, M. / Persson, C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 26, 2007 / Release: Aug 14, 2007
RevisionDateData content typeGroupProviderType
1.0Aug 14, 2007Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelAdvisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosolic acyl coenzyme A thioester hydrolase
B: Cytosolic acyl coenzyme A thioester hydrolase
C: Cytosolic acyl coenzyme A thioester hydrolase
D: Cytosolic acyl coenzyme A thioester hydrolase
E: Cytosolic acyl coenzyme A thioester hydrolase
F: Cytosolic acyl coenzyme A thioester hydrolase
G: Cytosolic acyl coenzyme A thioester hydrolase
H: Cytosolic acyl coenzyme A thioester hydrolase
I: Cytosolic acyl coenzyme A thioester hydrolase
J: Cytosolic acyl coenzyme A thioester hydrolase
K: Cytosolic acyl coenzyme A thioester hydrolase
L: Cytosolic acyl coenzyme A thioester hydrolase


Theoretical massNumber of molelcules
Total (without water)256,67112
Polymers256,67112
Non-polymers00
Water0
1
A: Cytosolic acyl coenzyme A thioester hydrolase
B: Cytosolic acyl coenzyme A thioester hydrolase
C: Cytosolic acyl coenzyme A thioester hydrolase
D: Cytosolic acyl coenzyme A thioester hydrolase
E: Cytosolic acyl coenzyme A thioester hydrolase
K: Cytosolic acyl coenzyme A thioester hydrolase


Theoretical massNumber of molelcules
Total (without water)128,3366
Polymers128,3366
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
MethodPISA
2
F: Cytosolic acyl coenzyme A thioester hydrolase
G: Cytosolic acyl coenzyme A thioester hydrolase
H: Cytosolic acyl coenzyme A thioester hydrolase
I: Cytosolic acyl coenzyme A thioester hydrolase
J: Cytosolic acyl coenzyme A thioester hydrolase
L: Cytosolic acyl coenzyme A thioester hydrolase


Theoretical massNumber of molelcules
Total (without water)128,3366
Polymers128,3366
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)80.950, 81.600, 105.100
Angle α, β, γ (deg.)79.61, 89.70, 74.12
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131A
141B
151C
161D
171E
181F
191G
201H
211I
221J
231K
241L
251A
261B
271C
281D
291E
301F
311G
321H
331I
341J
351K
361L
12A
22B
32C
42D
52H
62I
72L
13E
23F
33G
43K
14A
24B
34C
44D
54E
64G
74H
84I
94J
104K
114L
124F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRILE2AA212 - 27437 - 99
211THRILE2BB212 - 27437 - 99
311THRILE2CC212 - 27437 - 99
411THRILE2DD212 - 27437 - 99
511THRILE2EE212 - 27437 - 99
611THRILE2FF212 - 27437 - 99
711THRILE2GG212 - 27437 - 99
811THRILE2HH212 - 27437 - 99
911THRILE2II212 - 27437 - 99
1011THRILE2JJ212 - 27437 - 99
1111THRILE2KK212 - 27437 - 99
1211THRILE2LL212 - 27437 - 99
1321LYSVAL3AA276 - 323101 - 148
1421LYSVAL3BB276 - 323101 - 148
1521LYSVAL3CC - D276 - 323101 - 148
1621LYSVAL3DD276 - 323101 - 148
1721LYSVAL3EE276 - 323101 - 148
1821LYSVAL3FF276 - 323101 - 148
1921LYSVAL3GG276 - 323101 - 148
2021LYSVAL3HH276 - 323101 - 148
2121LYSVAL3II276 - 323101 - 148
2221LYSVAL3JJ276 - 323101 - 148
2321LYSVAL3KK276 - 323101 - 148
2421LYSVAL3LL276 - 323101 - 148
2531LEUHIS2AA332 - 365157 - 190
2631LEUGLN2BB332 - 363157 - 188
2731LEUHIS2CC332 - 365157 - 190
2831LEUALA2DD332 - 360157 - 185
2931LEUALA2EE332 - 360157 - 185
3031LEUALA2FF332 - 360157 - 185
3131LEUALA2GG332 - 360157 - 185
3231LEUGLN2HH332 - 363157 - 188
3331LEULYS2II332 - 361157 - 186
3431LEUALA2JJ332 - 360157 - 185
3531LEUGLN2KK332 - 363157 - 188
3631LEUHIS2LL332 - 365157 - 190
112PROASN2AA208 - 21133 - 36
212PROASN2BB208 - 21133 - 36
312PROASN2CC208 - 21133 - 36
412PROASN2DD208 - 21133 - 36
512PROASN2HH208 - 21133 - 36
612PROASN2II208 - 21133 - 36
712PROASN2LL208 - 21133 - 36
113ASNASN2EE207 - 21133 - 36
213GLUASN2FF209 - 21133 - 36
313PROASN2GG208 - 21133 - 36
413PROASN2KK208 - 21133 - 36
114SERSER2AA324 - 331149 - 156
214SERSER2BB324 - 331149 - 156
314SERSER2CC324 - 331149 - 156
414SERSER2DD324 - 331149 - 156
514SERSER2EE324 - 331149 - 156
614SERSER2GG324 - 331149 - 156
714SERSER2HH324 - 331149 - 156
814SERSER2II324 - 331149 - 156
914SERSER2JJ324 - 331149 - 156
1014SERSER2KK324 - 331149 - 156
1114SERSER2LL324 - 331149 - 156
1214SERSER2FF324 - 331149 - 156

NCS ensembles:
ID
1
2
3
4
DetailsTwo biological hexamers consist of chains A,B,C,D,E,K and F,G,H,I,J,L

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Components

#1: Protein/peptide
Cytosolic acyl coenzyme A thioester hydrolase / Long chain acyl-CoA thioester hydrolase / CTE-II / CTE-IIa / Brain acyl-CoA hydrolase / Acyl-CoA thioesterase 7


Mass: 21389.254 Da / Num. of mol.: 12 / Fragment: C-terminal domain: Residues 209-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACOT7, BACH / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00154, palmitoyl-CoA hydrolase

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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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris, 0.2mM MgCl2, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2007 / Details: mirrors
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 59646 / Num. obs: 59646 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.65
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.43 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VPM
Resolution: 2.8→19.87 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 37.88 / SU ML: 0.325 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 3.269 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOPS CONTAINING RESIDUES 306-309, 325-303 AND THE C-TERMINUS HAVE POOR DENSITY BUT EFFORT WAS MADE TO BUILD AS MUCH OF THOSE REGIONS AS POSSIBLE. SOME OF THE SIDECHAINS ARE MISSING FROM THE MODEL IN THESE REGIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23921 2984 5 %RANDOM
Rwork0.21593 ---
Obs0.2171 56660 95.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.951 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14037 0 0 0 14037
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0150.02214279
r_bond_other_d
r_angle_refined_deg1.421.95719255
r_angle_other_deg
r_dihedral_angle_1_deg6.18951809
r_dihedral_angle_2_deg29.65323.565589
r_dihedral_angle_3_deg18.167152536
r_dihedral_angle_4_deg12.3251599
r_chiral_restr0.0860.22216
r_gen_planes_refined0.0040.0210509
r_gen_planes_other
r_nbd_refined0.2380.255880
r_nbd_other
r_nbtor_refined0.3270.510002
r_nbtor_other
r_xyhbond_nbd_refined0.1650.35745
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.3730.2539
r_symmetry_vdw_other
r_symmetry_hbond_refined0.3450.356
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it2.05429237
r_mcbond_other
r_mcangle_it3.658314696
r_scbond_it5.64545425
r_scangle_it8.91164559
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Refine LS restraints NCS

Refinement-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A532tight positional0.070.05
12B532tight positional0.050
13C532tight positional0.050
14D532tight positional0.050
15E532tight positional0.060
16F532tight positional0.050
17G532tight positional0.060
18H532tight positional0.040
19I532tight positional0.040
110J532tight positional0.060
111K532tight positional0.060
112L532tight positional0.040
21A16tight positional0.020.05
22B16tight positional0.020
23C16tight positional0.030
24D16tight positional0.030
25H16tight positional0.020
26I16tight positional0.030
27L16tight positional0.020
31E12tight positional0.030.05
32F12tight positional0.040
33G12tight positional0.060
34K12tight positional0.060
41A32tight positional0.030.05
42B32tight positional0.020
43C32tight positional0.030
44D32tight positional0.020
45E32tight positional0.030
46G32tight positional0.030
47H32tight positional0.030
48I32tight positional0.020
49J32tight positional0.020
410K32tight positional0.030
411L32tight positional0.040
412F32tight positional0.050
11A334medium positional0.070.5
12B334medium positional0.050
13C334medium positional0.050
14D334medium positional0.060
15E334medium positional0.060
16F334medium positional0.050
17G334medium positional0.050
18H334medium positional0.040
19I334medium positional0.040
110J334medium positional0.060
111K334medium positional0.060
112L334medium positional0.050
21A15medium positional0.030.5
22B15medium positional0.020.03
23C15medium positional0.030
24D15medium positional0.040
25H15medium positional0.030
26I15medium positional0.040
27L15medium positional0.020
31E12medium positional0.050.5
32F12medium positional0.040.04
33G12medium positional0.030
34K12medium positional0.060
41A9medium positional0.030.5
42B9medium positional0.050.06
43C9medium positional0.060.01
44D9medium positional0.040
45E9medium positional0.040
46G9medium positional0.030
47H9medium positional0.040
48I9medium positional0.050
49J9medium positional0.040
410K9medium positional0.040
411L9medium positional0.050
412F9medium positional0.060
11A155loose positional0.065
12B155loose positional0.050.03
13C155loose positional0.050
14D155loose positional0.060
15E155loose positional0.060
16F155loose positional0.050
17G155loose positional0.050
18H155loose positional0.050
19I155loose positional0.040
110J155loose positional0.050
111K155loose positional0.060
112L155loose positional0.040
11A532tight thermal0.180.5
12B532tight thermal0.140
13C532tight thermal0.140
14D532tight thermal0.130
15E532tight thermal0.150
16F532tight thermal0.110
17G532tight thermal0.140
18H532tight thermal0.090
19I532tight thermal0.110
110J532tight thermal0.160
111K532tight thermal0.150
112L532tight thermal0.110
21A16tight thermal0.050.5
22B16tight thermal0.070.03
23C16tight thermal0.050
24D16tight thermal0.050
25H16tight thermal0.040
26I16tight thermal0.050
27L16tight thermal0.070
31E12tight thermal0.140.5
32F12tight thermal0.150.04
33G12tight thermal0.230
34K12tight thermal0.170
41A32tight thermal0.050.5
42B32tight thermal0.060.02
43C32tight thermal0.050
44D32tight thermal0.050
45E32tight thermal0.070
46G32tight thermal0.050
47H32tight thermal0.050
48I32tight thermal0.050
49J32tight thermal0.050
410K32tight thermal0.090
411L32tight thermal0.060
412F32tight thermal0.080
11A334medium thermal0.122
12B334medium thermal0.10.01
13C334medium thermal0.110
14D334medium thermal0.10
15E334medium thermal0.120
16F334medium thermal0.090
17G334medium thermal0.110
18H334medium thermal0.070
19I334medium thermal0.080
110J334medium thermal0.120
111K334medium thermal0.130
112L334medium thermal0.080
21A15medium thermal0.052
22B15medium thermal0.030.13
23C15medium thermal0.040.01
24D15medium thermal0.030
25H15medium thermal0.020
26I15medium thermal0.040
27L15medium thermal0.030
31E12medium thermal0.082
32F12medium thermal0.090.17
33G12medium thermal0.060.01
34K12medium thermal0.10
41A9medium thermal0.072
42B9medium thermal0.070.22
43C9medium thermal0.050.02
44D9medium thermal0.040
45E9medium thermal0.070
46G9medium thermal0.050
47H9medium thermal0.030
48I9medium thermal0.040
49J9medium thermal0.040
410K9medium thermal0.090
411L9medium thermal0.080
412F9medium thermal0.040
11A155loose thermal0.1410
12B155loose thermal0.120.06
13C155loose thermal0.110
14D155loose thermal0.120
15E155loose thermal0.120
16F155loose thermal0.120
17G155loose thermal0.120
18H155loose thermal0.080
19I155loose thermal0.090
110J155loose thermal0.10
111K155loose thermal0.130
112L155loose thermal0.10
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 220 -
Rwork0.326 4182 -
Obs--97.37 %
Refinement TLS params.

Method: refined / Refinement-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)
18.8722-1.98790.52692.86611.3082.51990.17390.602-0.373-0.1644-0.41860.39870.0953-0.35920.2446-0.3233-0.0086-0.0021-0.2155-0.0505-0.2303-3.575-23.472-26.167
25.90231.0691-1.72073.3417-1.36616.30620.2867-0.12610.76550.0506-0.33690.5346-0.0302-0.01630.0501-0.29810.02250.0605-0.2639-0.0945-0.13163.409-8.436-13.042
34.49070.8791-1.2093.5169-1.09412.22790.3292-0.0491.0157-0.06010.11070.329-0.3262-0.0254-0.44-0.21220.02820.1129-0.3843-0.04290.072424.7435.306-20.157
44.39970.95390.03664.84660.78757.9083-0.35870.9422-0.6572-0.43160.5228-0.2189-0.19490.0739-0.1642-0.2935-0.11930.0964-0.0226-0.1025-0.353135.276-26.132-42.158
54.49430.0231-0.92158.1246-1.71242.8419-0.35740.6643-0.8077-0.09410.0175-0.34630.1744-0.14560.3398-0.3237-0.08860.078-0.2647-0.212-0.106319.376-39.626-35.345
610.5870.339-3.34414.48750.03494.0961-0.13820.8104-1.28330.09990.1224-0.48570.2176-0.15750.0159-0.2017-0.2082-0.1556-0.0582-0.2720.11830.866.09729.618
78.20192.2932-0.34986.1606-2.47963.44770.24830.9947-2.20720.1417-0.0688-0.4611-0.00990.0812-0.1794-0.0914-0.3634-0.0079-0.0413-0.67320.5888-16.021-6.75525.86
86.25691.5278-0.17995.482-0.33251.8253-0.13460.41032.0518-0.12640.13270.0804-0.21650.08780.0019-0.0174-0.2241-0.0596-0.14570.06680.7293-19.6840.69430.271
98.5469-0.8567-1.95455.54881.77736.3998-0.0398-0.50141.75350.41310.0544-0.63080.05390.2765-0.0147-0.0897-0.2418-0.1618-0.02-0.24050.1325-4.59628.90739.802
109.93840.48790.81962.650.1234.5884-0.21622.3507-0.9005-0.3130.39440.69690.1432-0.1927-0.1782-0.0576-0.3449-0.0590.7039-0.4993-0.2616-36.3775.84314.978
115.1831-0.3130.48453.18360.71642.39020.03350.05450.5836-0.30510.3149-0.0645-0.350.0226-0.3484-0.3048-0.03990.1291-0.2586-0.0243-0.239940.781-6.059-27.109
127.73711.5509-0.70344.75910.9113.2297-0.15980.97481.0738-0.0243-0.01491.0297-0.34050.00010.1747-0.1539-0.0865-0.07790.15140.08580.046-43.49222.62525.051
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDAuth asym-IDAuth seq-ID
11A208 - 365
22B208 - 363
33C208 - 365
44D208 - 360
55E207 - 360
66F209 - 360
77G208 - 360
88H208 - 363
99I208 - 361
1010J212 - 360
1111K208 - 363
1212L208 - 365

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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. See below links for details.
  • 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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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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.

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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