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- PDB-2w0c: X-ray structure of the entire lipid-containing bacteriophage PM2 -

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Basic information

Entry
Database: PDB / ID: 2w0c
TitleX-ray structure of the entire lipid-containing bacteriophage PM2
Components
  • MAJOR CAPSID PROTEIN P2
  • PROTEIN 2
  • PROTEIN P3
  • PROTEIN P6
KeywordsVIRUS / MEMBER OF PRD1-ADENO VIRAL LINEAGE / MEMBRANE-CONTAINING BACTERIOPHAGE / VIRUS VIRION / MEMBRANE / TRANSMEMBRANE / CAPSID PROTEIN
Function / homology
Function and homology information


viral inner membrane / viral capsid, major subunit / virion component / virion membrane / membrane
Similarity search - Function
: / Bacteriophage PM2, Viral membrane protein P3 / Viral coat protein P2, N-terminal / : / Viral coat protein P2 N-terminal domain / Phage PM2 spike protein P1 / Spike protein P1, first jelly-roll domain / Spike protein P1, second jelly-roll domain
Similarity search - Domain/homology
Major capsid protein P2 / Protein P6 / Spike protein P1 / Protein P3
Similarity search - Component
Biological speciesPSEUDOALTEROMONAS PHAGE PM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
AuthorsAbrescia, N.G.A. / Grimes, J.M. / Kivela, H.M. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
Citation
Journal: Mol.Cell / Year: 2008
Title: Insights Into Virus Evolution and Membrane Biogenesis from the Structure of the Marine Lipid-Containing Bacteriophage Pm2
Authors: Abrescia, N.G.A. / Grimes, J.M. / Kivela, H.M. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Preliminary Crystallographic Analysis of the Major Capsid Protein P2 of the Lipid-Containing Bacteriophage Pm2.
Authors: Abrescia, N.G.A. / Kivela, H.M. / Grimes, J.M. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
#2: Journal: J.Struct.Biol. / Year: 2008
Title: Selenomethionine Labeling of Large Biological Macromolecular Complexes: Probing the Structure of Marine Bacterial Virus Pm2.
Authors: Kivela, H.M. / Abrescia, N.G.A. / Bamford, J.K.H. / Grimes, J.M. / Stuart, D.I. / Bamford, D.H.
History
DepositionAug 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,75227
Polymers397,31116
Non-polymers44111
Water00
1
A: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)23,865,0901620
Polymers23,838,639960
Non-polymers26,451660
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: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules
x 5


  • icosahedral pentamer
  • 1.99 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,988,758135
Polymers1,986,55380
Non-polymers2,20455
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 2.39 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)2,386,509162
Polymers2,383,86496
Non-polymers2,64566
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
6
A: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
G: MAJOR CAPSID PROTEIN P2
H: MAJOR CAPSID PROTEIN P2
I: MAJOR CAPSID PROTEIN P2
J: MAJOR CAPSID PROTEIN P2
L: PROTEIN 2
P: PROTEIN P3
Q: PROTEIN P3
R: PROTEIN P3
S: PROTEIN P3
T: PROTEIN P6
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 23.9 MDa, 960 polymers
Theoretical massNumber of molelcules
Total (without water)23,865,0901620
Polymers23,838,639960
Non-polymers26,451660
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)946.900, 677.600, 1067.600
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.438676, 0.122701, -0.890229), (-0.610434, 0.76769, -0.194991), (0.659495, 0.628964, 0.411668)340.15449, 179.20263, 3.48827
3generate(-0.469566, -0.4119, -0.780926), (-0.865003, 0.391806, 0.313462), (0.176856, 0.822695, -0.540274)508.25494, 108.45263, 341.96649
4generate(-0.469566, -0.865003, 0.176856), (-0.4119, 0.391806, 0.822695), (-0.780926, 0.313462, -0.540274)271.99224, -114.47591, 547.66927
5generate(0.438676, -0.610434, 0.659495), (0.122701, 0.76769, 0.628964), (-0.890229, -0.194991, 0.411668)-42.12659, -181.50332, 336.32235
6generate(-0.762275, -0.330162, -0.556713), (-0.330162, -0.541457, 0.773186), (-0.556713, 0.773186, 0.303732)515.81567, -119.82934, 291.32649
7generate(-0.499999, -0.697147, 0.513797), (0.695602, 0.030124, 0.717795), (-0.515886, 0.716295, 0.469875)195.41646, -326.46893, 241.57454
8generate(0.545072, -0.273383, 0.792565), (0.760137, 0.559944, -0.329626), (-0.353678, 0.782128, 0.513018)-97.79865, -81.95449, 196.09466
9generate(0.928684, 0.355502, -0.105658), (-0.225742, 0.31581, -0.921577), (-0.294255, 0.879706, 0.37354)41.38366, 275.80334, 217.7385
10generate(0.1207, 0.320411, -0.939558), (-0.899584, -0.364893, -0.240001), (-0.419737, 0.874179, 0.244194)420.61817, 252.39539, 276.59501
11generate(-0.858366, -0.412463, 0.305094), (-0.412463, 0.201164, -0.888486), (0.305094, -0.888486, -0.342799)323.86941, 307.74251, 265.69377
12generate(0.076445, -0.230073, 0.970166), (-0.889687, -0.455003, -0.037799), (0.450125, -0.860255, -0.239476)-40.95784, 200.39121, 209.058
13generate(0.813799, 0.442955, 0.376195), (-0.137463, -0.482241, 0.865186), (0.564655, -0.7558, -0.331558)-52.80017, -183.90951, 207.1749
14generate(0.334697, 0.676519, -0.655972), (0.804661, 0.157092, 0.572576), (0.490406, -0.719475, -0.49179)304.70811, -314.06912, 262.64686
15generate(-0.698757, 0.147841, -0.699915), (0.634701, 0.57946, -0.511253), (0.329989, -0.801479, -0.498737)537.50271, -10.21146, 298.81351
16generate(0.620641, 0.742625, 0.251619), (0.742625, -0.659707, 0.115299), (0.251619, 0.115299, -0.960934)19.41793, -187.95733, 429.66623
17generate(-0.015122, 0.804519, -0.593734), (0.804519, -0.342811, -0.485005), (-0.593734, -0.485005, -0.642067)364.48989, -53.16908, 532.56569
18generate(-0.889304, 0.242328, -0.387833), (0.242328, -0.469508, -0.849022), (-0.387833, -0.849022, 0.358813)501.44689, 157.36721, 241.45044
19generate(-0.793816, -0.167018, 0.584775), (-0.167018, -0.864708, -0.473693), (0.584775, -0.473693, 0.658524)241.019, 152.69754, -41.36812
20generate(0.139382, 0.142182, 0.979978), (0.142182, -0.982257, 0.12229), (0.979978, 0.12229, -0.157125)-56.89128, -60.72477, 74.95563
21generate(0.641647, -0.58844, -0.491964), (-0.682824, -0.146101, -0.715825), (0.349344, 0.795232, -0.495546)198.31257, 323.21518, 293.88695
22generate(0.316231, -0.682436, -0.658998), (-0.682436, -0.646172, 0.341676), (-0.658998, 0.341676, -0.670059)309.40559, 62.2709, 553.49677
23generate(0.1207, -0.899584, -0.419738), (0.320411, -0.364893, 0.874179), (-0.939558, -0.240001, 0.244194)292.3798, -284.46677, 388.22748
24generate(0.32527, -0.939792, -0.104832), (0.939817, 0.309017, 0.145784), (-0.104611, -0.145942, 0.983747)170.76427, -237.81816, 26.47563
25generate(0.647233, -0.747494, -0.14947), (0.319784, 0.444238, -0.836894), (0.691973, 0.493867, 0.526562)112.62752, 137.74994, -31.83002
26generate(-0.020948, -0.273612, -0.961612), (0.967246, -0.248916, 0.049754), (-0.252974, -0.929073, 0.269865)456.4743, -220.0278, 234.42616
27generate(-0.476345, -0.817439, -0.323864), (0.609067, -0.041115, -0.792052), (0.634139, -0.574545, 0.517461)396.96224, 64.55239, -17.17523
28generate(0.076445, -0.889687, 0.450125), (-0.230073, -0.455003, -0.860255), (0.970166, -0.037799, -0.239476)87.31419, 261.59852, 97.37493
29generate(0.873486, -0.390512, 0.290729), (-0.390512, -0.918601, -0.0606), (0.290729, -0.0606, -0.954884)-44.54677, 98.79953, 419.77222
30generate(0.813293, -0.009756, -0.581772), (0.349472, -0.791233, 0.501817), (-0.465213, -0.611437, -0.640094)183.60673, -198.8619, 504.47454
31generate(-0.458153, 0.054074, 0.887227), (0.42798, 0.88825, 0.166867), (-0.779056, 0.456166, -0.430097)94.32278, -133.08243, 520.09182
32generate(0.351133, 0.54333, 0.76256), (-0.244426, 0.839368, -0.485507), (-0.90386, -0.015912, 0.427533)-48.73496, 172.25578, 335.33822
33generate(0.32527, 0.939817, -0.104611), (-0.939792, 0.309017, -0.145942), (-0.104832, 0.145784, 0.983747)170.73061, 237.83669, 26.52623
34generate(-0.499999, 0.695602, -0.515886), (-0.697147, 0.030124, 0.716295), (0.513797, 0.717795, 0.469875)449.42552, -26.97028, 20.42353
35generate(-0.984181, 0.148183, 0.097104), (0.148183, 0.38811, 0.909622), (0.097104, 0.909622, -0.403929)402.20289, -256.2109, 325.46384
36generate(-0.162545, 0.807978, 0.566349), (-0.712402, -0.493233, 0.499204), (0.682687, -0.322325, 0.655778)109.99335, 29.85089, -61.71843
37generate(-0.191018, 0.956545, 0.220302), (0.317795, -0.152081, 0.935883), (0.928719, 0.248781, -0.274935)201.47014, -299.12323, 115.02675
38generate(-0.522415, 0.849455, 0.074223), (0.849455, 0.51088, 0.132017), (0.074223, 0.132017, -0.988465)308.67841, -215.0126, 474.55786
39generate(-0.698757, 0.634701, 0.329989), (0.147841, 0.57946, -0.801479), (-0.699915, -0.511253, -0.498737)283.45999, 165.94475, 520.01512
40generate(-0.476345, 0.609067, 0.634139), (-0.817439, -0.041115, -0.574545), (-0.323864, -0.792052, 0.517461)160.66587, 317.2787, 188.57814
41generate(0.641647, -0.682824, 0.349344), (-0.58844, -0.146101, 0.795232), (-0.491964, -0.715825, -0.495546)-9.21512, -69.79119, 474.56269
42generate(0.928684, -0.225742, -0.294255), (0.355502, 0.31581, 0.879706), (-0.105658, -0.921577, 0.37354)87.89869, -293.35925, 177.21262
43generate(0.351133, -0.244426, -0.90386), (0.54333, 0.839368, -0.015912), (0.76256, -0.485507, 0.427533)362.3148, -112.77096, -22.57351
44generate(-0.292852, -0.713054, -0.637018), (-0.284527, 0.701034, -0.653908), (0.912843, -0.010249, -0.408182)434.79948, 222.4068, 151.30194
45generate(-0.113304, -0.983999, 0.137505), (-0.983999, 0.09198, -0.152594), (0.137505, -0.152594, -0.978676)205.18136, 248.96976, 458.54901
46generate(-0.458153, 0.42798, -0.779056), (0.054074, 0.88825, 0.456166), (0.887227, 0.166867, -0.430097)505.35174, -124.13829, 162.21136
47generate(-0.976018, -0.217658, 0.003697), (-0.217658, 0.975448, -0.03355), (0.003697, -0.03355, -0.99943)423.48653, 55.02319, 492.40839
48generate(-0.292852, -0.284527, 0.912843), (-0.713054, 0.701034, -0.010249), (-0.637018, -0.653908, -0.408182)52.49759, 155.67171, 484.16729
49generate(0.647233, 0.319784, 0.691973), (-0.747494, 0.444238, 0.493867), (-0.14947, -0.836894, 0.526562)-94.92097, 38.71443, 148.87698
50generate(0.545072, 0.760137, -0.353678), (-0.273383, 0.559944, 0.782128), (0.792565, -0.329626, 0.513018)184.95828, -134.21766, -50.10272
51generate(-0.162545, -0.712402, 0.682687), (0.807978, -0.493233, -0.322325), (0.566349, 0.499204, 0.655778)81.27915, -94.04215, -36.72266
52generate(0.813799, -0.137463, 0.564655), (0.442955, -0.482241, -0.7558), (0.376195, 0.865186, -0.331558)-99.2944, 91.2822, 247.66951
53generate(0.813293, 0.349472, -0.465213), (-0.009756, -0.791233, -0.611437), (-0.581772, 0.501817, -0.640094)154.85886, 152.89992, 529.52091
54generate(-0.163364, 0.075476, -0.983675), (0.075476, -0.993191, -0.088741), (-0.983675, -0.088741, 0.156555)492.50776, 5.65741, 419.32248
55generate(-0.766465, -0.580799, -0.274233), (0.580863, -0.809017, 0.089941), (-0.274097, -0.090355, 0.957448)447.033, -146.96118, 69.3647
56generate(-0.020948, 0.967246, -0.252974), (-0.273612, -0.248916, -0.929073), (-0.961612, 0.049754, 0.269865)281.68724, 287.92747, 386.63511
57generate(-0.766465, 0.580863, -0.274097), (-0.580799, -0.809017, -0.090355), (-0.274233, 0.089941, 0.957448)447.01219, 147.00969, 69.39598
58generate(-0.871574, 0.17948, 0.45623), (0.17948, -0.749169, 0.637599), (0.45623, 0.637599, 0.620743)289.43176, -195.84484, -4.42819
59generate(-0.191018, 0.317795, 0.928719), (0.956545, -0.152081, 0.248781), (0.220302, 0.935883, -0.274935)26.71674, -266.82281, 267.1851
60generate(0.334697, 0.804661, 0.490406), (0.676519, 0.157092, -0.719475), (-0.655972, 0.572576, -0.49179)21.93037, 32.16492, 508.87551

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Components

#1: Protein
MAJOR CAPSID PROTEIN P2


Mass: 30233.723 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) PSEUDOALTEROMONAS PHAGE PM2 (virus) / References: UniProt: P15794
#2: Protein PROTEIN 2


Mass: 37540.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PSEUDOALTEROMONAS PHAGE PM2 (virus) / References: UniProt: Q9XJR3
#3: Protein
PROTEIN P3 / PROTEIN III


Mass: 10767.355 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) PSEUDOALTEROMONAS PHAGE PM2 (virus) / References: UniProt: Q9XJR6
#4: Protein PROTEIN P6 / PROTEIN VI


Mass: 14363.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PSEUDOALTEROMONAS PHAGE PM2 (virus) / References: UniProt: Q9XJR1
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
Nonpolymer detailsCALCIUM (CA): THESE CALCIUM WERE DERIVED FROM ATOMIC STRUCTURE OF P2 AND P1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 718

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Sample preparation

CrystalDescription: THE STARTING MODEL FOR MANUAL MOLECULAR REPLACEMENT WAS A PRELIMINARY CRYO-EM RECONSTRUCTION OF PM2
Crystal growpH: 7.4
Details: 20MG/ML VIRUS WITH 20MM MOPS PH 7.4, 100MM NACL, 5MM CACL2 MIXED 1:1 WITH 1.5% PEG 8K, 500MM NACL, 2.5MM CACL2, 100MM MOPS PH 7.4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1273.151
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-110.7291
SYNCHROTRONESRF ID2920.9756
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.72911
20.97561
ReflectionResolution: 7→96 Å / Num. obs: 874109 / % possible obs: 85.1 % / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.32 / Net I/σ(I): 3.1
Reflection shellResolution: 7→7.25 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 0.45 / % possible all: 56.7

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 7→96 Å / σ(F): 0
Details: THE ATOMIC MODELS COMPOSING THE ICOSAHEDRAL ASYMMETRIC UNIT WAS REFINED AS RIGID BODY AGAINST THE EXPERIMENTAL DATA USING STRICT 60-NCS AND AB AS TARGET FUNCTION IN XPLOR. FOR DETAILS PLEASE ...Details: THE ATOMIC MODELS COMPOSING THE ICOSAHEDRAL ASYMMETRIC UNIT WAS REFINED AS RIGID BODY AGAINST THE EXPERIMENTAL DATA USING STRICT 60-NCS AND AB AS TARGET FUNCTION IN XPLOR. FOR DETAILS PLEASE SEE PRIMARY REFERENCE. THE ATOMIC MODELS CORRESPONDING TO P3, P6 AND P1 (RESIDUES 1- 88) HAVE BEEN BUILT INTO THE AVERAGED VIRUS MAP AND THEN REGULARIZED. PLEASE REFER TO PRIMARY SEQUENCE FOR MORE DETAILS.
RfactorNum. reflection% reflection
Rwork0.419 --
obs0.419 851677 82.9 %
Refinement stepCycle: LAST / Resolution: 7→96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26436 0 11 0 26447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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