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- PDB-2w4z: Caulobacter bacteriophage 5 -

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Basic information

Entry
Database: PDB / ID: 2w4z
TitleCaulobacter bacteriophage 5
ComponentsCAULOBACTER BACTERIOPHAGE 5
KeywordsVIRUS / ASSEMBLY / CALCIUM ION / RNA
Function / homologyPorin - #220 / Porin / Beta Barrel / Mainly Beta / ADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesUNCLASSIFIED LEVIVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsPlevka, P. / Kazaks, A. / Dishlers, A. / Liljas, L. / Tars, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The Structure of Bacteriophage Phicb5 Reveals a Role of the RNA Genome and Metal Ions in Particle Stability and Assembly.
Authors: Plevka, P. / Kazaks, A. / Voronkova, T. / Kotelovica, S. / Dishlers, A. / Liljas, L. / Tars, K.
History
DepositionDec 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAULOBACTER BACTERIOPHAGE 5
B: CAULOBACTER BACTERIOPHAGE 5
C: CAULOBACTER BACTERIOPHAGE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,69910
Polymers40,4973
Non-polymers1,2027
Water00
1
A: CAULOBACTER BACTERIOPHAGE 5
B: CAULOBACTER BACTERIOPHAGE 5
C: CAULOBACTER BACTERIOPHAGE 5
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)2,501,935600
Polymers2,429,817180
Non-polymers72,119420
Water0
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: CAULOBACTER BACTERIOPHAGE 5
B: CAULOBACTER BACTERIOPHAGE 5
C: CAULOBACTER BACTERIOPHAGE 5
hetero molecules
x 5


  • icosahedral pentamer
  • 208 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)208,49550
Polymers202,48515
Non-polymers6,01035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: CAULOBACTER BACTERIOPHAGE 5
B: CAULOBACTER BACTERIOPHAGE 5
C: CAULOBACTER BACTERIOPHAGE 5
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 250 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)250,19460
Polymers242,98218
Non-polymers7,21242
Water0
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
Unit cell
Length a, b, c (Å)273.600, 273.600, 640.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.750599, 0.136828, 0.646435), (0.493697, 0.534095, -0.686299), (-0.439163, 0.834278, 0.33334)-0.00387, 0.00449, 0.00283
3generate(0.347061, 0.71509, 0.606791), (0.935646, -0.219755, -0.276176), (-0.064146, 0.663592, -0.74534)-0.00433, 0.00304, 0.00921
4generate(0.347061, 0.935646, -0.064146), (0.71509, -0.219755, 0.663592), (0.606791, -0.276176, -0.74534)-0.00075, -0.00235, 0.01033
5generate(0.750599, 0.493697, -0.439163), (0.136828, 0.534095, 0.834278), (0.646435, -0.686299, 0.33334)0.00193, -0.00423, 0.00464
6generate(-0.656724, 0.754131, 4.6E-5), (0.754131, 0.656724, 0.000101), (4.6E-5, 0.000101, -1)-0.00077, 0.00035, 0.01152
7generate(-0.120644, 0.312957, -0.942074), (0.890228, 0.454024, 0.036822), (0.439247, -0.834218, -0.333379)0.00516, 0.00038, 0.00869
8generate(0.477674, -0.63531, -0.606802), (0.876184, 0.39502, 0.276153), (0.064256, -0.663581, 0.74534)0.00437, -0.00092, 0.00231
9generate(0.311376, -0.780198, 0.542527), (0.731407, 0.561254, 0.387347), (-0.606703, 0.276197, 0.745403)-0.00205, -0.00176, 0.00118
10generate(-0.38972, 0.078524, 0.91758), (0.655974, 0.722996, 0.216737), (-0.646387, 0.686375, -0.333276)-0.00522, -0.00097, 0.00688
11generate(0.44581, -0.658161, 0.606694), (-0.658161, -0.700392, -0.276179), (0.606694, -0.276179, -0.745418)-0.00259, 0.00384, 0.01033
12generate(-0.256745, 0.21563, 0.942118), (-0.718509, -0.694541, -0.036842), (0.646395, -0.686379, 0.333252)-0.00555, 0.00246, 0.00464
13generate(-0.5, 0.866025, 8.9E-5), (-0.866025, -0.5, -8.8E-5), (-3.1E-5, -0.000121, 1)-0.00093, 0.00202
14generate(0.052215, 0.3942, -0.91754), (-0.896848, -0.385618, -0.216709), (-0.439246, 0.834209, 0.333403)0.00489, 0.00312, 0.00283
15generate(0.636758, -0.547799, -0.542638), (-0.768381, -0.509467, -0.387343), (-0.06427, 0.663596, -0.745325)0.00387, 0.00425, 0.00921
16generate(-0.789086, -0.09597, -0.606739), (-0.09597, -0.956332, 0.276078), (-0.606739, 0.276078, 0.745418)0.00383, 0.00092, 0.00118
17generate(-0.37321, -0.665416, -0.646479), (-0.665416, -0.293577, 0.686319), (-0.646479, 0.686319, -0.333213)0.00473, -0.00222, 0.00688
18generate(-0.324735, -0.945805, -7.9E-5), (-0.945805, 0.324735, 0.000111), (-7.9E-5, 0.000111, -1)0.00136, 0.00097, 0.01152
19generate(-0.710652, -0.549649, 0.439158), (-0.549649, 0.044119, -0.83423), (0.439158, -0.83423, -0.333467)-0.00163, 0.00609, 0.00869
20generate(-0.997637, -0.024422, 0.064222), (-0.024422, -0.747624, -0.663673), (0.064222, -0.663673, 0.745261)-0.00011, 0.00605, 0.00231
21generate(-0.058398, -0.330277, 0.942076), (0.960746, -0.274972, -0.036845), (0.271214, 0.902944, 0.33337)-0.00488, 0.00173, 0.00265
22generate(-0.620615, 0.601564, 0.502949), (0.601564, -0.046143, 0.797491), (0.502949, 0.797491, -0.333242)-0.00347, -0.00333, 0.0066
23generate(-0.38972, 0.655974, -0.646387), (0.078524, 0.722996, 0.686375), (0.91758, 0.216737, -0.333276)0.00305, -0.00361, 0.00729
24generate(0.315198, -0.242239, -0.91759), (0.11445, 0.969521, -0.216634), (0.9421, -0.036735, 0.333315)0.00567, 0.00127, 0.00378
25generate(0.519966, -0.851776, 0.064135), (0.659693, 0.352743, -0.663609), (0.542623, 0.387364, 0.745325)0.00077, 0.00457, 0.00091
26generate(-0.210678, -0.260846, -0.942112), (-0.838311, 0.543944, 0.036862), (0.502841, 0.797549, -0.333267)0.0059, 0.00047, 0.0066
27generate(0.126828, -0.954127, -0.271215), (-0.376881, 0.206566, -0.902935), (0.917538, 0.216733, -0.333394)0.00288, 0.00626, 0.00729
28generate(-0.256745, -0.718509, 0.646395), (0.21563, -0.694541, -0.686379), (0.942118, -0.036842, 0.333252)-0.00266, 0.00609, 0.00378
29generate(-0.831311, 0.120392, 0.542612), (0.120392, -0.914078, 0.387256), (0.542612, 0.387256, 0.745389)-0.00306, 0.0002, 0.00091
30generate(-0.80284, 0.403243, -0.439139), (-0.53098, -0.148652, 0.834244), (0.271124, 0.902938, 0.333458)0.00222, -0.00328, 0.00265
31generate(0.762892, 0.009577, -0.646455), (0.586932, -0.429562, 0.686285), (-0.27112, -0.902987, -0.333331)0.00374, -0.0022, 0.00886
32generate(0.861254, -0.429823, 0.271099), (-0.072913, 0.423435, 0.902987), (-0.502917, -0.797468, 0.333345)-0.001, -0.00446, 0.00492
33generate(0.315198, 0.11445, 0.9421), (-0.242239, 0.969521, -0.036735), (-0.917589, -0.216634, 0.333315)-0.00549, 0.00028, 0.00422
34generate(-0.120644, 0.890228, 0.439247), (0.312957, 0.454024, -0.834218), (-0.942074, 0.036822, -0.333379)-0.00353, 0.00546, 0.00774
35generate(0.156046, 0.825414, -0.542533), (0.825414, -0.410657, -0.387367), (-0.542533, -0.387367, -0.745389)0.00217, 0.00393, 0.01061
36generate(-0.493817, 0.581545, 0.64649), (-0.709367, 0.16059, -0.686301), (-0.502935, -0.797506, 0.333227)-0.00429, 0.00511, 0.00492
37generate(-0.367466, 0.782385, -0.502834), (-0.151769, -0.583858, -0.797544), (-0.91757, -0.216756, 0.33329)0.00206, 0.00663, 0.00422
38generate(0.331267, -0.051915, -0.942108), (-0.051915, -0.997975, 0.036739), (-0.942108, 0.036739, -0.333292)0.00557, 0.00234, 0.00774
39generate(0.636758, -0.768381, -0.06427), (-0.547799, -0.509467, 0.663596), (-0.542638, -0.387343, -0.745325)0.00139, -0.00183, 0.01061
40generate(0.126828, -0.376881, 0.917538), (-0.954127, 0.206566, 0.216733), (-0.271215, -0.902935, -0.333394)-0.0047, -0.00012, 0.00886
41generate(-0.058398, 0.960746, 0.271214), (-0.330277, -0.274972, 0.902944), (0.942076, -0.036845, 0.33337)-0.00266, -0.00353, 0.00378
42generate(0.311376, 0.731407, -0.606703), (-0.780198, 0.561254, 0.276197), (0.542527, 0.387347, 0.745403)0.00264, -0.00094, 0.00091
43generate(0.861254, -0.072913, -0.502917), (-0.429823, 0.423435, -0.797468), (0.271099, 0.902987, 0.333345)0.00301, 0.00538, 0.00266
44generate(0.831322, -0.340672, 0.439143), (0.236643, -0.497968, -0.834283), (0.502896, 0.797478, -0.333354)-0.00207, 0.00669, 0.0066
45generate(0.262946, 0.298165, 0.917582), (0.298165, -0.929607, 0.216629), (0.917582, 0.216629, -0.333339)-0.00558, 0.00118, 0.00729
46generate(0.762892, 0.586932, -0.27112), (0.009577, -0.429562, -0.902987), (-0.646455, 0.686285, -0.333331)0.00084, 0.00702, 0.00688
47generate(0.981459, 0.191674, -2.5E-5), (0.191674, -0.981459, -2.0E-6), (-2.5E-5, -2.0E-6, -1)-0.00024, 0.00251, 0.01152
48generate(0.831322, 0.236643, 0.502896), (-0.340672, -0.497968, 0.797478), (0.439143, -0.834283, -0.333354)-0.00318, -0.00264, 0.00869
49generate(0.519966, 0.659693, 0.542623), (-0.851776, 0.352743, 0.387364), (0.064135, -0.663609, 0.745325)-0.00391, -0.00131, 0.00231
50generate(0.477674, 0.876184, 0.064256), (-0.63531, 0.39502, -0.663581), (-0.606802, 0.276153, 0.74534)-0.00143, 0.00467, 0.00119
51generate(-0.493817, -0.709367, -0.502935), (0.581545, 0.16059, -0.797506), (0.64649, -0.686301, 0.333227)0.00398, 0.0056, 0.00464
52generate(-0.5, -0.866025, -3.1E-5), (0.866025, -0.5, -0.000121), (8.9E-5, -8.8E-5, 1)0.00128, 0.00181
53generate(-0.80284, -0.53098, 0.271124), (0.403243, -0.148652, 0.902938), (-0.439139, 0.834244, 0.333458)-0.00067, -0.00378, 0.00283
54generate(-0.983822, -0.167252, -0.064197), (-0.167252, 0.729083, 0.663675), (-0.064197, 0.663675, -0.745261)0.00081, -0.00346, 0.00921
55generate(-0.792835, -0.277501, -0.542591), (-0.057055, 0.920205, -0.387257), (0.60676, -0.276073, -0.745403)0.00369, 0.00234, 0.01033
56generate(-0.210678, -0.838311, 0.502841), (-0.260846, 0.543944, 0.797549), (-0.942112, 0.036862, -0.333267)-0.00168, -0.00398, 0.00774
57generate(-0.792835, -0.057055, 0.60676), (-0.277501, 0.920205, -0.276073), (-0.542591, -0.387257, -0.745403)-0.00321, 0.00172, 0.01061
58generate(-0.889736, 0.367251, -0.271103), (0.367251, 0.223185, -0.902948), (-0.271103, -0.902948, -0.333449)0.00131, 0.00615, 0.00886
59generate(-0.367466, -0.151769, -0.91757), (0.782385, -0.583858, -0.216756), (-0.502834, -0.797544, 0.33329)0.00564, 0.00318, 0.00492
60generate(0.052215, -0.896848, -0.439246), (0.3942, -0.385618, 0.834209), (-0.91754, -0.216709, 0.333403)0.00378, -0.00308, 0.00422
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I).

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Components

#1: Protein CAULOBACTER BACTERIOPHAGE 5


Mass: 13498.981 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: LEVIVIRUS COAT PROTEIN / Source: (natural) UNCLASSIFIED LEVIVIRUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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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: 5.7 Å3/Da / Density % sol: 74 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS-HCL PH 8.0, 5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 25, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 163899 / % possible obs: 79 % / Observed criterion σ(I): 0.5 / Redundancy: 1.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 3.6
Reflection shellResolution: 3.6→3.76 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 0.9 / % possible all: 48

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CB5-VLP MODEL

Resolution: 3.6→50 Å / Cross valid method: NONE / σ(F): 0
Stereochemistry target values: STANDARD CRYSTALLOGRAPHIC RESIDUAL
RfactorNum. reflection% reflection
Rwork0.296 --
obs0.296 163899 79 %
Solvent computationBsol: 17.45 Å2 / ksol: 0.77 e/Å3
Displacement parametersBiso mean: 63.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.792 Å2-3.32 Å20 Å2
2--6.792 Å20 Å2
3----13.584 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a1.19 Å1.08 Å
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 70 0 2932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009367
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.44809
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.6→3.76 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.3754 12622 -
obs--48 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_PARAMPROTEIN_TOP
X-RAY DIFFRACTION2ION_PARAMION_TOP
X-RAY DIFFRACTION3DNA-RNA_REP_PARAMDNA-RNA-ALLATOM_TOP

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