[English] 日本語
Yorodumi
- PDB-1x36: T=1 capsid of an amino-terminal deletion mutant of SeMV CP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x36
TitleT=1 capsid of an amino-terminal deletion mutant of SeMV CP
ComponentsCoat protein
KeywordsVIRUS / T=1 capsid / N-ARM / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral 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: 2.7 Å
AuthorsSangita, V. / Satheshkumar, P.S. / Savithri, H.S. / Murthy, M.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a mutant T=1 capsid of Sesbania mosaic virus: role of water molecules in capsid architecture and integrity.
Authors: Sangita, V. / Satheshkumar, P.S. / Savithri, H.S. / Murthy, M.R.
History
DepositionApr 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_asym_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_asym_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)25,2612
Polymers25,2211
Non-polymers401
Water3,117173
1
A: Coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,515,638120
Polymers1,513,23460
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
  • 126 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)126,30310
Polymers126,1035
Non-polymers2005
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 152 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)151,56412
Polymers151,3236
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
  • 1.52 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,515,638120
Polymers1,513,23460
Non-polymers2,40560
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)193.451, 313.506, 321.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.51309255, 0.79771205, -0.3168462), (-0.79899392, 0.30901901, -0.5158643), (-0.31359967, 0.51784432, 0.79592243)39.98618, 69.45986, 25.74585
3generate(-0.27474025, 0.4917313, -0.82626759), (-0.49508726, -0.80901172, -0.31684165), (-0.82426112, 0.32202541, 0.46571798)107.75429, 45.69419, 69.66729
4generate(-0.27474025, -0.49508726, -0.82426112), (0.4917313, -0.80901172, 0.32202541), (-0.82626759, -0.31684165, 0.46571798)109.65109, -38.45366, 71.06639
5generate(0.51309255, -0.79899392, -0.31359967), (0.79771205, 0.30901901, 0.51784432), (-0.3168462, -0.5158643, 0.79592243)43.05528, -66.69422, 28.00963
6generate(-0.78830927, 0.32413115, -0.52297944), (0.32413115, -0.50370524, -0.80076216), (-0.52297944, -0.80076216, 0.2920145)68.23349, 108.66984, 94.97061
7generate(-0.49944825, -0.79950305, -0.33368596), (0.81988545, -0.3117613, -0.48020074), (0.27989158, -0.51341968, 0.81120955)45.76156, 66.027, 25.95599
8generate(0.4871787, -0.81827491, 0.30509522), (0.82036329, 0.30902311, -0.4811536), (0.29943444, 0.4846967, 0.82183217)-38.33387, 64.79302, 22.37101
9generate(0.80808668, 0.29375765, 0.51059021), (0.32490431, 0.50074504, -0.80230393), (-0.49135843, 0.81422408, 0.30920227)-67.83577, 106.67321, 89.16999
10generate(0.01979176, 0.99980342, -0.00118807), (0.01821599, -0.0015487, -0.99983288), (-0.99963817, 0.01976681, -0.01824306)-1.97352, 133.79057, 134.03901
11generate(-0.48529485, -0.82107441, -0.30054237), (-0.82107441, 0.30980464, 0.47943498), (-0.30054237, 0.47943498, -0.82450978)41.44556, -61.54233, 239.1113
12generate(0.50128228, -0.79648731, 0.33811839), (-0.81916984, -0.31097276, 0.48193021), (-0.27870569, -0.51855946, -0.80834351)-42.72896, -60.51151, 239.16753
13generate(0.78755891, 0.32884188, 0.52116599), (-0.32297775, -0.49999332, 0.80354965), (0.52482029, -0.80116771, -0.28756558)-69.30334, -102.45941, 171.19259
14generate(-0.02208953, 0.99974647, -0.00436513), (-0.01821876, 0.00396293, 0.99982617), (0.99958998, 0.02216522, 0.0181266)-1.55269, -129.41545, 129.12554
15generate(-0.80875642, 0.28905911, -0.51220883), (-0.32605942, 0.5044456, 0.79951228), (0.4894878, 0.81362121, -0.31372317)66.89389, -104.1273, 171.1016
16generate(0.27360412, 0.49694326, 0.82352182), (0.49694326, -0.8060994, 0.32132718), (0.82352182, 0.32132718, -0.46750472)-109.43651, -38.36845, 192.40017
17generate(-0.51492658, 0.79827831, 0.31241377), (0.79827831, 0.31371505, 0.51413482), (0.31241377, 0.51413482, -0.79878847)-42.77625, -66.21629, 235.61269
18generate(-0.99999736, -0.00229827, 6.38E-6), (-0.00229827, 0.99998193, -0.0055544), (6.38E-6, -0.0055544, -0.99998457)0.12546, 0.73125, 263.25117
19generate(-0.5112569, -0.79841685, 0.31803604), (-0.79841685, 0.30430375, -0.51954765), (0.31803604, -0.51954765, -0.79304686)-40.02009, 69.95495, 237.12016
20generate(0.27587211, -0.48986861, 0.82699657), (-0.48986861, -0.8119159, -0.31752372), (0.82699657, -0.31752372, -0.46395621)-107.73311, 45.79001, 193.33183
21generate(0.8294884, 0.29219141, -0.47599704), (-0.29178046, -0.49999997, -0.81539205), (-0.47624906, 0.81524488, -0.32948843)62.02149, 110.62466, 173.23164
22generate(0.34141767, 0.50549323, -0.79240808), (0.50549323, -0.80951242, -0.29860716), (-0.79240808, -0.29860716, -0.53190525)103.23018, 43.23458, 202.33209
23generate(0.01979176, 0.01821599, -0.99963817), (0.99980342, -0.0015487, 0.01976681), (-0.00118807, -0.99983288, -0.01824306)131.59244, -0.46919, 136.21115
24generate(0.30908674, -0.49623973, -0.81130236), (0.50803023, 0.80731279, -0.30025214), (0.80397181, -0.31936217, 0.50163446)107.91258, 39.91048, 66.24571
25generate(0.80950678, -0.32691361, -0.48767435), (-0.29021251, 0.49925297, -0.81640871), (0.51036798, 0.80241758, 0.30927424)64.91536, 108.57025, 89.12563
26generate(-0.31024838, 0.5028451, -0.80677924), (0.49438096, 0.81021256, 0.31486993), (0.81199348, -0.30116841, -0.49996418)105.16704, -41.05773, 198.03631
27generate(-0.30795061, -0.50988622, -0.80323251), (-0.49243483, 0.80779833, -0.32399042), (0.81404813, 0.29576661, -0.49984772)106.91772, 43.09452, 196.71371
28generate(0.50128228, -0.81916984, -0.27870569), (-0.79648731, -0.31097276, -0.51855946), (0.33811839, 0.48193021, -0.80834351)38.50742, 71.17208, 236.93929
29generate(0.99911793, 0.00241371, 0.04192298), (0.00241371, -0.99999709, 5.062E-5), (0.04192298, 5.062E-5, -0.99912084)-5.52316, 4.37271, 263.12267
30generate(0.4975644, 0.81946387, -0.28444443), (0.80021417, -0.30706645, 0.51513831), (0.33479389, -0.48393094, -0.80853194)35.67476, -64.98912, 239.0793
31generate(-0.49940006, -0.81875907, 0.28325459), (0.7971966, -0.30625631, 0.52027364), (-0.33923026, 0.48563428, 0.80565636)-35.39831, -65.66663, 24.53675
32generate(0.30911653, -0.50470778, 0.80605026), (0.49057492, 0.81071506, 0.31949544), (-0.81472892, 0.29666672, 0.4982024)-104.94567, -41.66741, 65.44663
33generate(0.30908674, 0.50803023, 0.80397181), (-0.49623973, 0.80731279, -0.31936217), (-0.81130236, -0.30025214, 0.50163446)-106.88976, 42.48664, 66.30181
34generate(-0.49944825, 0.81988545, 0.27989158), (-0.79950305, -0.3117613, -0.51341968), (-0.33368596, -0.48020074, 0.81120955)-38.54391, 70.49749, 25.92046
35generate(-0.99912057, -0.00011544, -0.04192936), (-0.00011544, -0.99998485, 0.00550379), (-0.04192936, 0.00550379, 0.99910542)5.64023, 3.65509, 0.10824
36generate(-0.01983996, 0.02372256, 0.99952169), (-0.99979709, -0.00395629, -0.01975152), (0.00348584, -0.99971075, 0.02379624)-131.54767, 4.85876, 130.67736
37generate(-0.34258359, 0.50910078, 0.78959033), (-0.50363332, -0.80900097, 0.30310214), (0.79308888, -0.29382618, 0.53355057)-104.95969, -35.90264, 61.98964
38generate(-0.83016078, 0.29292362, 0.47437204), (0.29292362, -0.49479133, 0.81815481), (0.47437204, 0.81815481, 0.32495211)-62.96756, -104.43048, 87.02982
39generate(-0.80875642, -0.32605942, 0.4894878), (0.28905911, 0.5044456, 0.81362121), (-0.51220883, 0.79951228, -0.31372317)-63.60297, -106.02162, 171.19324
40generate(-0.30795061, -0.49243483, 0.81404813), (-0.50988622, 0.80779833, 0.29576661), (-0.80323251, -0.32399042, -0.49984772)-105.98781, -38.47716, 198.1689
41generate(0.82948839, -0.29178046, -0.47624906), (0.29219141, -0.49999997, 0.81524488), (-0.47599704, -0.81539205, -0.32948843)63.33342, -104.03602, 176.80233
42generate(0.80808668, 0.32490431, -0.49135843), (0.29375765, 0.50074504, 0.81422408), (0.51059021, -0.80230393, 0.30920227)63.97302, -106.09316, 92.64905
43generate(0.30911653, 0.49057492, -0.81472892), (-0.50470778, 0.81071506, 0.29666672), (0.80605026, 0.31949544, 0.4982024)106.20269, -38.60234, 65.29836
44generate(0.02213773, -0.02371979, -0.99947351), (-0.99975279, 0.00154206, -0.02218051), (0.00206736, 0.99971746, -0.02367979)131.66245, 5.16642, 132.54799
45generate(0.34374523, -0.50724201, -0.79028145), (-0.50724201, -0.80852438, 0.29831841), (-0.79028145, 0.29831841, -0.53522085)105.16779, -35.27382, 201.46124
46generate(-0.49940006, 0.7971966, -0.33923026), (-0.81875907, -0.30625631, 0.48563428), (0.28325459, 0.52027364, 0.80565636)42.99491, -61.0094, 24.42316
47generate(-0.78681119, -0.32769701, -0.52301322), (-0.32769701, -0.49629005, 0.80393461), (-0.52301322, 0.80393461, 0.28310123)69.66519, -102.5179, 92.62987
48generate(0.02213773, -0.99975279, 0.00206736), (-0.02371979, 0.00154206, 0.99971746), (-0.99947351, -0.02218051, -0.02367979)1.97641, -129.3955, 134.84644
49generate(0.80950678, -0.29021251, 0.51036798), (-0.32691361, 0.49925297, 0.80241758), (-0.48767435, -0.81640871, 0.30927424)-66.52785, -104.49828, 92.731
50generate(0.4871787, 0.82036329, 0.29943444), (-0.81827491, 0.30902311, 0.4846967), (0.30509522, -0.4811536, 0.82183217)-41.17702, -62.23334, 24.48566
51generate(-0.01983996, -0.99979709, 0.00348584), (0.02372256, -0.00395629, -0.99971075), (0.99952169, -0.01975152, 0.02379624)1.79235, 133.77944, 128.47109
52generate(0.78755891, -0.32297775, 0.52482029), (0.32884188, -0.49999332, -0.80116771), (0.52116599, 0.80354965, -0.28756558)-68.35699, 108.7148, 167.67886
53generate(0.4975644, 0.80021417, 0.33479389), (0.81946387, -0.30706645, -0.48393094), (-0.28444443, 0.51513831, -0.80853194)-45.78756, 66.50772, 236.92913
54generate(-0.48906092, 0.81756562, -0.30398334), (0.81756562, 0.30820595, -0.48641089), (-0.30398334, -0.48641089, -0.81914503)38.31046, 65.48695, 240.52037
55generate(-0.8088344, -0.29490252, -0.50874298), (0.32577045, 0.49553833, -0.80518034), (0.48955136, -0.81699098, -0.30473792)67.71646, 107.06315, 173.48961
56generate(-0.31024838, 0.49438096, 0.81199348), (0.5028451, 0.81021256, -0.30116841), (-0.80677924, 0.31486993, -0.49996418)-107.87813, 40.02504, 196.78549
57generate(-0.8088344, 0.32577045, 0.48955136), (-0.29490252, 0.49553833, -0.81699098), (-0.50874298, -0.80518034, -0.30473792)-65.03868, 108.65531, 173.52428
58generate(-0.82881865, -0.2910363, 0.47786767), (-0.2910363, -0.50519067, -0.81245324), (0.47786767, -0.81245324, 0.33400932)-62.149, 110.24918, 89.40814
59generate(-0.34258359, -0.50363332, 0.79308888), (0.50910078, -0.80900097, -0.29382618), (0.78959033, 0.30310214, 0.53355057)-103.20252, 42.60397, 60.68272
60generate(-0.02208953, -0.01821876, 0.99958998), (0.99974647, 0.00396293, 0.02216522), (-0.00436513, 0.99982617, 0.0181266)-131.46468, -0.79693, 127.04557

-
Components

#1: Protein Coat protein


Mass: 25220.562 Da / Num. of mol.: 1 / Fragment: residues 32-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sesbania mosaic virus / Genus: Sobemovirus / Plasmid: pSBETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / 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.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 4% PEG 3350, 0.1M MgCl2, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 2004
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 738540 / Num. obs: 515695 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.7→2.8 Å / % possible all: 96.9

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 293017.75 / 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
Rfree0.247 23946 5 %RANDOM
Rwork0.245 ---
obs0.245 482008 91.1 %-
all-515695 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.8316 Å2 / ksol: 0.37639 e/Å3
Displacement parametersBiso mean: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--7.1 Å20 Å2
3----7.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 1 173 1636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.77
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 3729 5 %
Rwork0.311 71579 -
obs--86.1 %
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://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