[English] 日本語
Yorodumi
- PDB-1vak: T=1 capsid structure of Sesbania mosaic virus coat protein deleti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vak
TitleT=1 capsid structure of Sesbania mosaic virus coat protein deletion mutant CP-N(delta)65
Componentscoat protein
KeywordsVIRUS / T=1 Capsid / SeMV / Icosahedral virus
Function / homology
Function and homology information


viral capsid / structural molecule activity / metal ion binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSesbania mosaic virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSangita, V. / Lokesh, G.L. / Satheshkumer, P.S. / Vijay, C.S. / Saravanan, V. / Savithri, H.S. / Murthy, M.R.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: T=1 capsid structures of Sesbania mosaic virus coat protein mutants: determinants of T=3 and T=1 capsid assembly
Authors: Sangita, V. / Lokesh, G.L. / Satheshkumar, P.S. / Vijay, C.S. / Saravanan, V. / Savithri, H.S. / Murthy, M.R.
History
DepositionFeb 18, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5112
Polymers21,4711
Non-polymers401
Water1,910106
1
A: coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,290,677120
Polymers1,288,27360
Non-polymers2,40560
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: coat protein
hetero molecules
x 5


  • icosahedral pentamer
  • 108 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)107,55610
Polymers107,3565
Non-polymers2005
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: coat protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 129 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)129,06812
Polymers128,8276
Non-polymers2406
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: coat protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 1.29 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,290,677120
Polymers1,288,27360
Non-polymers2,40560
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)188.239, 193.954, 269.054
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.46213991, -0.5176399, 0.72005252), (0.85017876, 0.48956165, -0.19371489), (-0.25223554, 0.70169675, 0.66633243)-26.48506, -22.77588, 33.52765
3generate(-0.40813599, 0.01261981, 0.91283391), (0.85797824, -0.33634495, 0.38825947), (0.31192684, 0.9416543, 0.12644696)-2.79349, -62.93792, 46.56692
4generate(-0.40813599, 0.85797824, 0.31192684), (0.01261981, -0.33634495, 0.9416543), (0.91283391, 0.38825947, 0.12644696)38.33377, -64.98354, 21.09799
5generate(0.46213991, 0.85017877, -0.25223554), (-0.5176399, 0.48956165, 0.70169675), (0.72005252, -0.19371489, 0.66633243)40.06024, -26.08577, -7.68195
6generate(-0.40655063, -0.01855047, 0.91343991), (-0.01855047, -0.99942014, -0.02855297), (0.91343991, -0.02855297, 0.40597077)-2.90206, 2.7477, 1.94123
7generate(-0.4340565, 0.84232304, 0.31951033), (-0.85105662, -0.49971083, 0.16121948), (0.29546165, -0.20194301, 0.93376733)38.91346, 25.04437, -7.98972
8generate(0.43493847, 0.86125338, -0.2628139), (-0.85881605, 0.30902879, -0.40857827), (-0.27067235, 0.4034152, 0.87406673)41.93725, 64.37132, 20.09142
9generate(0.99951277, 0.01207946, -0.02878049), (-0.0311055, 0.30914806, -0.95050509), (-0.00258415, 0.9509372, 0.30937317)1.99055, 66.38004, 47.37746
10generate(0.4794439, -0.53166922, 0.69818435), (0.48820719, -0.49951785, -0.71563654), (0.72923747, 0.68396619, 0.02007395)-25.72167, 28.29455, 36.16003
11generate(-0.99960637, 0.02805353, 0.00031399), (0.02805353, 0.99935591, 0.02237765), (0.00031399, 0.02237765, -0.99974954)84.73651, -2.72079, 136.86328
12generate(-0.43818668, 0.5313904, -0.72499426), (0.85695139, 0.49042703, -0.15847915), (0.27134248, -0.69072829, -0.67027434)110.58272, -25.47473, 102.82604
13generate(0.4321426, -0.02175484, -0.90154284), (0.85295616, -0.31470227, 0.4164472), (-0.29277732, -0.9489411, -0.11744033)85.77789, -64.65448, 88.89874
14generate(0.40861599, -0.86695427, -0.28534762), (0.02158911, -0.30337066, 0.95262802), (-0.91245103, -0.39541944, -0.10524533)44.60144, -66.11496, 114.32843
15generate(-0.47625354, -0.836171, 0.27203055), (-0.48822875, 0.50876196, 0.70907965), (-0.73131064, 0.20488856, -0.65054241)43.95783, -27.83784, 143.97215
16generate(0.406157, -0.00950306, -0.91375389), (-0.00950306, -0.99993578, 0.00617531), (-0.91375389, 0.00617531, -0.40622123)87.71511, -0.01284, 134.98311
17generate(0.41010327, -0.85607354, -0.31456859), (-0.85607354, -0.48027785, 0.19097456), (-0.31456859, 0.19097456, -0.92982542)46.53844, 23.22031, 145.42365
18generate(-0.45894508, -0.85211835, 0.25152283), (-0.85211835, 0.34201843, -0.3961284), (0.25152283, -0.3961284, -0.88307336)44.62791, 63.23515, 118.23054
19generate(-0.99999276, -0.00310343, 0.00220127), (-0.00310343, 0.33056755, -0.94377723), (0.00220127, -0.94377723, -0.33057479)84.62382, 64.73253, 90.98374
20generate(-0.46533027, 0.51766146, -0.71797935), (0.51766146, -0.49880576, -0.69513986), (-0.71797935, -0.69513986, -0.03586397)111.25317, 25.64313, 101.3374
21generate(0.47615546, 0.53027976, 0.70148368), (0.83503706, -0.02259397, -0.54972959), (-0.27566118, 0.84752161, -0.4535615)-25.81185, 2.23584, 111.17336
22generate(0.49394392, 0.50535639, 0.70755518), (0.50535639, -0.8290531, 0.23934468), (0.70755518, 0.23934468, -0.66489082)-26.98134, -37.79671, 83.96436
23generate(0.4794439, 0.48820719, 0.72923747), (-0.53166922, -0.49951785, 0.68396619), (0.69818435, -0.71563654, 0.02007395)-27.85075, -24.27402, 37.48121
24generate(0.45269394, 0.50253178, 0.73656636), (-0.84290562, 0.51060527, 0.16968313), (-0.2908235, -0.69767045, 0.65473478)-27.21858, 24.11601, 35.96204
25generate(0.45066157, 0.52853406, 0.71941358), (0.00176531, 0.80536044, -0.59278279), (-0.89269313, 0.26841441, 0.36201197)-25.95847, 40.5, 81.50629
26generate(0.43734494, -0.55883462, 0.70458021), (-0.84121066, 0.02278694, 0.54022716), (-0.31795287, -0.82896599, -0.46013189)-24.37489, -1.31671, 113.42162
27generate(-0.45071495, -0.00556955, 0.89265056), (-0.50564853, 0.82567545, -0.25015916), (-0.73564638, -0.56411792, -0.37496051)0.39287, 38.55636, 125.29591
28generate(-0.43818668, 0.85695139, 0.27134248), (0.5313904, 0.49042703, -0.69072829), (-0.72499426, -0.15847915, -0.67027434)42.38541, 24.75575, 145.05628
29generate(0.4576161, 0.83675358, -0.30071738), (0.83675358, -0.5196564, -0.17262868), (-0.30071738, -0.17262868, -0.9379597)43.57047, -23.64656, 145.39457
30generate(0.99872441, -0.03825029, -0.03296174), (-0.01156052, -0.80867387, 0.58814363), (-0.04915196, -0.58701234, -0.80808452)2.31033, -39.76023, 125.84328
31generate(-0.46087156, 0.55899362, -0.68929206), (-0.83551482, -0.01145533, 0.5493485), (0.29918623, 0.82909282, 0.47232689)109.10047, -2.18235, 23.43295
32generate(0.43612132, 0.02855335, -0.89943477), (-0.53442904, 0.81236377, -0.23334677), (0.72400538, 0.58245156, 0.3695489)85.46477, 38.62558, 12.46168
33generate(0.45269394, -0.84290562, -0.2908235), (0.50253178, 0.51060527, -0.69767045), (0.73656636, 0.16968313, 0.65473478)43.10781, 26.45409, -7.58939
34generate(-0.4340565, -0.85105662, 0.29546165), (0.84232304, -0.49971083, -0.20194301), (0.31951033, 0.16121948, 0.93376733)40.56547, -21.87623, -9.01036
35generate(-0.99867103, 0.01536476, 0.04919454), (0.01536476, -0.82236203, 0.56875708), (0.04919454, 0.56875708, 0.82103306)81.35118, -39.57452, 10.1625
36generate(-0.45262885, -0.53043876, -0.71677182), (0.84168842, 0.01126235, -0.53984606), (0.29442781, -0.84764844, 0.44136649)110.63583, 1.27729, 25.75969
37generate(-0.4793503, -0.52834018, -0.70077097), (0.53472119, -0.80898612, 0.24416124), (-0.69591418, -0.25767832, 0.67030242)110.67326, -39.37115, 52.06567
38generate(-0.49395116, -0.50225296, -0.70975645), (-0.50225296, -0.50151445, 0.70443255), (-0.70975645, 0.70443255, -0.00453439)111.90709, -26.92175, 98.83952
39generate(-0.47625354, -0.48822875, -0.73131064), (-0.836171, 0.50876196, 0.20488856), (0.27203055, 0.70907965, -0.65054241)112.6322, 21.42085, 101.44136
40generate(-0.45071495, -0.50564853, -0.73564638), (-0.00556955, 0.82567545, -0.56411792), (0.89265056, -0.25015916, -0.37496051)111.84652, 38.84882, 56.27554
41generate(0.47615546, 0.83503706, -0.27566118), (0.53027976, -0.02259397, 0.84752161), (0.70148368, -0.54972959, -0.4535615)41.06962, -80.48381, 69.75966
42generate(0.99951277, -0.0311055, -0.00258415), (0.01207946, 0.30914806, 0.9509372), (-0.02878049, -0.95050509, 0.30937317)0.19764, -65.59829, 48.49454
43generate(0.43612132, -0.53442904, 0.72400538), (0.02855335, 0.81236377, 0.58245156), (-0.89943477, -0.23334677, 0.3695489)-25.6527, -41.07665, 81.27794
44generate(-0.43543104, 0.02064246, 0.89998539), (0.55693508, 0.79162616, 0.25129931), (-0.70726454, 0.61065695, -0.35619511)-0.75711, -40.80695, 122.80431
45generate(-0.41068858, 0.86701906, 0.28215747), (0.86701906, 0.2755939, 0.41512162), (0.28215747, 0.41512162, -0.86490531)40.47955, -65.16192, 115.68562
46generate(-0.46087156, -0.83551482, 0.29918623), (0.55899362, -0.01145533, 0.82909282), (-0.68929206, 0.5493485, 0.47232689)41.4471, -80.43956, 65.33295
47generate(-0.9987895, 0.0394675, 0.02935742), (0.0394675, 0.28680624, 0.95717527), (0.02935742, 0.95717527, -0.28801675)82.71391, -67.1861, 86.91301
48generate(-0.43543104, 0.55693508, -0.70726454), (0.02064246, 0.79162616, 0.61065695), (0.89998539, 0.25129931, -0.35619511)109.25229, -42.67183, 54.67844
49generate(0.45066157, 0.00176531, -0.89269313), (0.52853406, 0.80536044, 0.26841441), (0.71941358, -0.59278279, 0.36201197)84.3871, -40.77463, 13.17633
50generate(0.43493847, -0.85881605, -0.27067235), (0.86125338, 0.30902879, 0.4034152), (-0.2628139, -0.40857827, 0.87406673)42.48119, -64.11637, 19.76118
51generate(-0.45262885, 0.84168842, 0.29442781), (-0.53043876, 0.01126235, -0.84764844), (-0.71677182, -0.53984606, 0.44136649)41.41751, 80.50631, 68.62072
52generate(0.4321426, 0.85295616, -0.29277732), (-0.02175484, -0.31470227, -0.9489411), (-0.90154284, 0.4164472, -0.11744033)44.10669, 65.87884, 114.69792
53generate(0.99872441, -0.01156052, -0.04915196), (-0.03825029, -0.80867387, -0.58701234), (-0.03296174, 0.58814363, -0.80808452)3.41841, 41.80687, 125.15288
54generate(0.46411977, -0.55712896, 0.68862193), (-0.55712896, -0.78800048, -0.26203541), (0.68862193, -0.26203541, -0.67611928)-24.41751, 41.55705, 85.53721
55generate(-0.43286587, -0.02979212, 0.90096591), (-0.86131816, -0.28125203, -0.42311738), (0.26600405, -0.95917137, 0.09608391)-0.93278, 65.47461, 50.59841
56generate(0.43734494, -0.84121066, -0.31795287), (-0.55883462, 0.02278694, -0.82896599), (0.70458021, 0.54022716, -0.46013189)45.61533, 80.43114, 70.07429
57generate(-0.43286587, -0.86131816, 0.26600405), (-0.02979212, -0.28125203, -0.95917137), (0.90096591, -0.42311738, 0.09608391)42.53132, 66.91963, 23.68215
58generate(-0.99941469, -0.01094552, 0.03241112), (-0.01094552, -0.79531605, -0.60609617), (0.03241112, -0.60609617, 0.79473074)82.53157, 41.95567, 12.67835
59generate(-0.4793503, 0.53472119, -0.69591418), (-0.52834018, -0.80898612, -0.25767832), (-0.70077097, 0.24416124, 0.67030242)110.33709, 40.03861, 52.26977
60generate(0.40861599, 0.02158911, -0.91245103), (-0.86695427, -0.30337066, -0.39541944), (-0.28534762, 0.95262803, -0.10524533)87.5216, 63.81775, 87.74241

-
Components

#1: Protein coat protein


Mass: 21471.213 Da / Num. of mol.: 1 / Fragment: residues 66-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sesbania mosaic virus / Genus: Sobemovirus / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EB06
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, magnesium chloride, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 2002 / Details: Osmic mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.05→20 Å / Num. all: 1386733 / Num. obs: 348643 / % possible obs: 53 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 / Rsym value: 0.082
Reflection shellResolution: 3.05→3.16 Å / Rmerge(I) obs: 0.122 / Num. unique all: 34159 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→20 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 274821.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 34232 10 %RANDOM
Rwork0.211 ---
obs0.211 341343 93.4 %-
all-375575 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.0119 Å2 / ksol: 0.311354 e/Å3
Displacement parametersBiso mean: 11.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å2-3.06 Å2
2--3.46 Å20 Å2
3----1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 1 106 1561
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.52.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.05→3.24 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 5403 10 %
Rwork0.286 48762 -
obs-48762 89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

+
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://pdbjlvh1.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