[English] 日本語
Yorodumi
- PDB-1bev: BOVINE ENTEROVIRUS VG-5-27 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bev
TitleBOVINE ENTEROVIRUS VG-5-27
Components(BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO ...) x 4
KeywordsVIRUS / COAT PROTEIN / BOVINE ENTEROVIRUS VG-5-27 / PICORNAVIRUS / Icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Few Secondary Structures / Irregular / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesBovine enterovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsSmyth, M. / Tate, J. / Lyons, C. / Hoey, E. / Martin, S. / Stuart, D.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Implications for viral uncoating from the structure of bovine enterovirus.
Authors: Smyth, M. / Tate, J. / Hoey, E. / Lyons, C. / Martin, S. / Stuart, D.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Analysis of Bovine Enterovirus
Authors: Smyth, M. / Fry, E. / Stuart, D. / Lyons, C. / Hoey, E. / Martin, S.J.
#2: Journal: J.Gen.Virol. / Year: 1990
Title: Chemically Synthesized Peptides Elicit Neutralizing Antibody to Bovine Enterovirus
Authors: Smyth, M.S. / Hoey, E.M. / Trudgett, A. / Martin, S.J. / Brown, F.
#3: Journal: J.Gen.Virol. / Year: 1988
Title: The Complete Nucleotide Sequence of a Bovine Enterovirus
Authors: Earle, J.A. / Skuce, R.A. / Fleming, C.S. / Hoey, E.M. / Martin, S.J.
History
DepositionApr 3, 1996Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _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
1: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
2: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
3: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
4: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9247
Polymers92,5044
Non-polymers4203
Water2,342130
1
1: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
2: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
3: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
4: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,575,445420
Polymers5,550,215240
Non-polymers25,230180
Water3,243180
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
1: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
2: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
3: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
4: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 465 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)464,62035
Polymers462,51820
Non-polymers2,10215
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
2: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
3: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
4: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 558 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)557,54542
Polymers555,02224
Non-polymers2,52318
Water32418
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
1: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
2: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
3: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
4: BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 5.58 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)5,575,445420
Polymers5,550,215240
Non-polymers25,230180
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)388.200, 392.600, 360.700
Angle α, β, γ (deg.)90.00, 112.70, 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(0.55149312, -0.69102, 0.46727583), (0.81438692, 0.32470864, -0.48097634), (0.18063577, 0.64579847, 0.74183223)17.19674, -52.10501, -2.95034
3generate(-0.17420625, -0.30370692, 0.93670395), (0.62668572, -0.76793573, -0.1324376), (0.75955065, 0.56394753, 0.324108)61.30759, -53.60011, -35.68199
4generate(-0.17420625, 0.62668572, 0.75955065), (-0.30370692, -0.76793573, 0.56394753), (0.93670395, -0.1324376, 0.324108)71.37287, -2.41913, -52.96092
5generate(0.55149312, 0.81438692, 0.18063577), (-0.69102, 0.32470864, 0.64579847), (0.46727583, -0.48097634, 0.74183223)33.48269, 30.70756, -30.90823
6generate(-0.38010991, -0.43591294, 0.81577961), (-0.43591294, -0.69346164, -0.57366442), (0.81577961, -0.57366442, 0.07357154)88.26123, 75.1111, -26.93174
7generate(-0.41727082, 0.64794807, 0.63721924), (-0.90877339, -0.29442003, -0.29571569), (-0.00399831, -0.70248142, 0.71169085)102.031, 105.44015, 16.77073
8generate(0.41266303, 0.91025203, -0.03391849), (-0.79437093, 0.34140711, -0.50241021), (-0.4457399, 0.23426998, 0.86396384)59.21395, 106.02543, 51.20504
9generate(0.96275128, -0.01149622, -0.27014406), (-0.25080587, 0.33532829, -0.90810316), (0.1010267, 0.9420312, 0.31995442)18.98179, 76.05811, 28.78414
10generate(0.47279066, -0.84347193, 0.25499824), (-0.02926665, -0.30425577, -0.95214069), (0.88068863, 0.44270028, -0.16853488)36.934, 56.952, -19.50705
11generate(-0.89787379, 0.41583, 0.14459623), (0.41583, 0.69314604, 0.5887563), (0.14459623, 0.5887563, -0.79527225)176.89653, -74.00978, 87.89797
12generate(-0.13040546, 0.84885236, -0.51229297), (0.9001669, 0.31794158, 0.29767886), (0.41556464, -0.42233023, -0.80557011)139.3626, -104.71227, 62.05373
13generate(0.52683811, 0.03490446, -0.84924866), (0.80913477, -0.3265544, 0.48853163), (-0.26027395, -0.9445337, -0.20028371)94.40203, -106.67694, 93.58231
14generate(0.16556864, -0.90116538, -0.40060953), (0.26853691, -0.34967036, 0.89756257), (-0.94893359, -0.25618666, 0.18410172)104.14881, -77.18868, 138.91229
15generate(-0.71495174, -0.66574044, 0.21362039), (0.0254612, 0.28053917, 0.95950482), (-0.69871005, 0.69143867, -0.18362142)155.13321, -56.99927, 135.39917
16generate(0.2779837, 0.02008295, -0.96037583), (0.02008295, -0.99968441, -0.01509188), (-0.96037583, -0.01509188, -0.27829929)124.9883, -1.10138, 166.30041
17generate(-0.00381684, -0.80578043, -0.5922021), (-0.80578043, -0.3482302, 0.47901318), (-0.5922021, 0.47901318, -0.64795296)131.55573, 51.37706, 151.39252
18generate(-0.76529489, -0.64144957, -0.0535368), (-0.64144957, 0.75308302, 0.14631618), (-0.0535368, 0.14631618, -0.98778813)175.22249, 54.25156, 118.16128
19generate(-0.95411366, 0.28597587, -0.08879706), (0.28597587, 0.7822778, -0.55340694), (-0.08879706, -0.55340694, -0.82816414)195.6426, 3.54964, 112.53113
20generate(-0.30933204, 0.69482545, -0.64925441), (0.69482545, -0.30099204, -0.6531626), (-0.64925441, -0.6531626, -0.38967593)164.59616, -30.66036, 142.28275
21generate(0.75146991, 0.20212977, 0.62804182), (0.65402176, -0.3535731, -0.66876124), (0.08688213, 0.91330697, -0.39789681)-11.44248, -25.79425, 70.94966
22generate(0.69248915, -0.048059, 0.71982575), (-0.048059, -0.99863534, -0.02043978), (0.71982575, -0.02043978, -0.6938538)-10.90456, 5.84879, 26.02982
23generate(0.47279066, -0.02926665, 0.88068863), (-0.84347193, -0.30425577, 0.44270028), (0.25499824, -0.95214069, -0.16853488)1.38438, 57.11654, 41.52059
24generate(0.39599029, 0.23253644, 0.88832342), (-0.63298338, 0.76995665, 0.08061511), (-0.66522457, -0.59421676, 0.45208705)8.44144, 57.15871, 96.01426
25generate(0.56822354, 0.37554729, 0.73217911), (0.29251862, 0.73947687, -0.60630588), (-0.76912604, 0.55869329, 0.31033359)0.51401, 5.91702, 114.20243
26generate(0.13859157, -0.82802995, 0.54328517), (-0.64003484, 0.34373735, 0.68716812), (-0.75574319, -0.44295715, -0.48232892)53.15112, 23.38416, 157.93353
27generate(-0.49976773, -0.01378529, 0.86604976), (0.05108753, 0.99766349, 0.04536111), (-0.86465154, 0.06691437, -0.49789576)97.07607, -7.56017, 169.44053
28generate(-0.13040546, 0.9001669, 0.41556464), (0.84885236, 0.31794158, -0.42233023), (-0.51229297, 0.29767886, -0.80557011)86.64483, -58.79872, 152.55374
29generate(0.73623228, 0.65077576, -0.18561506), (0.65077576, -0.75607579, -0.06957236), (-0.18561506, -0.06957236, -0.98015649)36.27302, -59.52156, 130.61012
30generate(0.90248158, -0.41730864, -0.10667943), (-0.26940714, -0.74013313, 0.61613533), (-0.33607557, -0.52731059, -0.78038244)15.57277, -8.72975, 133.93501
31generate(-0.49986104, 0.82235276, -0.27179934), (-0.83095565, -0.36685332, 0.41824795), (0.24423686, 0.43491905, 0.86671435)161.73397, 57.28505, -16.24916
32generate(0.34494672, 0.43691142, -0.83073472), (-0.68147633, 0.72519042, 0.09843208), (0.64544695, 0.53217222, 0.54789685)111.09119, 60.87624, -37.26765
33generate(0.39599029, -0.63298338, -0.66522457), (0.23253644, 0.76995665, -0.59421676), (0.88832342, 0.08061511, 0.45208705)96.70883, 11.08061, -55.51339
34generate(-0.41727082, -0.90877339, -0.00399831), (0.64794807, -0.29442003, -0.70248142), (0.63721924, -0.29571569, 0.71169085)138.46281, -23.28597, -45.77139
35generate(-0.97093739, -0.00932619, 0.23915186), (-0.00932619, -0.99700723, -0.07674382), (0.23915186, -0.07674382, 0.96794461)178.65056, 5.26994, -21.50476
36generate(-0.39020044, -0.19645258, -0.89952765), (0.81696873, 0.37668906, -0.43665483), (0.4246242, -0.90526887, 0.01351138)186.70346, -54.87503, 14.63261
37generate(-0.53766814, -0.37506713, -0.75514079), (0.6784478, -0.72421856, -0.12335341), (-0.50062117, -0.57864681, 0.64385271)192.88337, -59.16494, 69.06393
38generate(-0.73837548, -0.23791687, -0.63102869), (-0.23791687, -0.78364246, 0.57384672), (-0.63102869, 0.57384672, 0.52201794)205.40803, -9.3985, 88.70569
39generate(-0.71495174, 0.0254612, -0.69871005), (-0.66574044, 0.28053917, 0.69143867), (0.21362039, 0.95950482, -0.18362142)206.96879, 25.64876, 46.41364
40generate(-0.49976773, 0.05108753, -0.86465154), (-0.01378529, 0.99766349, 0.06691437), (0.86604976, 0.04536111, -0.49789576)195.40873, -2.45728, 0.63396
41generate(0.75146991, 0.65402176, 0.08688213), (0.20212977, -0.3535731, 0.91330697), (0.62804182, -0.66876124, -0.39789681)19.30442, -71.60611, 18.1668
42generate(0.96275128, -0.25080587, 0.1010267), (-0.01149622, 0.33532829, 0.9420312), (-0.27014406, -0.90810316, 0.31995442)-2.10689, -52.40178, 64.98681
43generate(0.34494672, -0.68147633, 0.64544695), (0.43691142, 0.72519042, 0.53217222), (-0.83073472, 0.09843208, 0.54789685)27.21946, -72.85107, 106.71396
44generate(-0.24815886, -0.04281768, 0.96777261), (0.92766857, 0.27723707, 0.25014122), (-0.27901291, 0.95984699, -0.02907822)66.75546, -104.69376, 85.68275
45generate(0.00308629, 0.78256553, 0.62256057), (0.78256553, -0.38947544, 0.48569545), (0.62256057, 0.48569545, -0.61361085)61.86369, -103.92433, 30.9576
46generate(-0.49986104, -0.83095565, 0.24423686), (0.82235276, -0.36685332, 0.43491905), (-0.27179934, 0.41824795, 0.86671435)132.41448, -104.92009, 34.08321
47generate(-0.90827142, 0.23332329, 0.34727981), (0.23332329, -0.40651258, 0.88335031), (0.34727981, 0.88335031, 0.31478401)166.39487, -72.94658, 5.05924
48generate(-0.24815886, 0.92766857, -0.27901291), (-0.04281768, 0.27723707, 0.95984699), (0.96777261, 0.25014122, -0.02907822)137.59366, -50.35902, -35.92438
49generate(0.56822354, 0.29251862, -0.76912604), (0.37554729, 0.73947687, 0.55869329), (0.73217911, -0.60630588, 0.31033359)85.81315, -68.37267, -32.22967
50generate(0.41266303, -0.79437093, -0.4457399), (0.91025203, 0.34140711, 0.23426998), (-0.03391849, -0.50241021, 0.86396384)82.61224, -102.09326, 11.0374
51generate(-0.39020044, 0.81696873, 0.4246242), (-0.19645258, 0.37668906, -0.90526887), (-0.89952765, -0.43665483, 0.01351138)111.46959, 70.59564, 143.78577
52generate(0.52683811, 0.80913477, -0.26027395), (0.03490446, -0.3265544, -0.9445337), (-0.84924866, 0.48853163, -0.20028371)60.93847, 50.26077, 151.02887
53generate(0.90248158, -0.26940714, -0.33607557), (-0.41730864, -0.74013313, -0.52731059), (-0.10667943, 0.61613533, -0.78038244)28.60629, 70.66283, 111.56053
54generate(0.21760346, -0.92814873, 0.3019746), (-0.92814873, -0.29249538, -0.2301877), (0.3019746, -0.2301877, -0.92510808)59.15503, 103.60687, 79.92466
55generate(-0.58131796, -0.25673152, 0.77211291), (-0.79165219, 0.39773869, -0.46377877), (-0.18803255, -0.88084781, -0.43445472)110.36737, 103.56535, 99.84095
56generate(0.13859157, -0.64003484, -0.75574319), (-0.82802995, 0.34373735, -0.44295715), (0.54328517, 0.68716812, -0.48232892)126.95757, 105.93049, 31.23085
57generate(-0.58131796, -0.79165219, -0.18803255), (-0.25673152, 0.39773869, -0.88084781), (0.77211291, -0.46377877, -0.43445472)164.91961, 75.08752, 6.19171
58generate(-0.99926945, 0.0232149, -0.03035847), (0.0232149, -0.26229436, -0.96470863), (-0.03035847, -0.96470863, 0.26156381)196.72665, 52.5472, 44.91652
59generate(-0.53766814, 0.6784478, -0.50062117), (-0.37506713, -0.72421856, -0.57864681), (-0.75514079, -0.12335341, 0.64385271)178.42243, 69.45949, 93.8889
60generate(0.16556864, 0.26853691, -0.94893359), (-0.90116538, -0.34967036, -0.25618666), (-0.40060953, 0.89756257, 0.18410172)135.30277, 102.45218, 85.43069

-
Components

-
BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO ... , 4 types, 4 molecules 1234

#1: Protein BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4


Mass: 31238.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine enterovirus (STRAIN VG-5-27) / Genus: Enterovirus / Species: Bovine enterovirus / Strain: VG-5-27 / Organ: KIDNEY / Plasmid: PBEV / Cell line (production host): BHK CELLS / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P12915
#2: Protein BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4


Mass: 27325.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine enterovirus (STRAIN VG-5-27) / Genus: Enterovirus / Species: Bovine enterovirus / Strain: VG-5-27 / Organ: KIDNEY / Plasmid: PBEV / Cell line (production host): BHK CELLS / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P12915
#3: Protein BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4


Mass: 26627.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine enterovirus (STRAIN VG-5-27) / Genus: Enterovirus / Species: Bovine enterovirus / Strain: VG-5-27 / Organ: KIDNEY / Plasmid: PBEV / Cell line (production host): BHK CELLS / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P12915
#4: Protein BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4


Mass: 7311.890 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine enterovirus (STRAIN VG-5-27) / Genus: Enterovirus / Species: Bovine enterovirus / Strain: VG-5-27 / Organ: KIDNEY / Plasmid: PBEV / Cell line (production host): BHK CELLS / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P12915

-
Non-polymers , 3 types, 133 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsRESIDUE GLY 4 1 IS MYRISTOYLATED.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity % sol: 60 %
Crystal grow
*PLUS
Method: other / Details: Smyth, M., (1993) J. Mol. Biol., 231, 930.

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87, 0.91, 0.95, 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.911
30.951
40.991
ReflectionResolution: 3→25 Å / Num. obs: 840070 / % possible obs: 42.5 % / Redundancy: 1.57 % / Rmerge(I) obs: 0.161

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 3→25 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.225 --
obs0.225 840070 42.5 %
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 26 130 6472
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.423
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
Refinement
*PLUS
Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.423

+
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