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- PDB-5cpy: Crystal structure of murine polyomavirus PTA strain VP1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5cpy
TitleCrystal structure of murine polyomavirus PTA strain VP1 in complex with the GD1a glycan
ComponentsVP1
KeywordsVIRAL PROTEIN / Murine Polyomavirus / Virus protein / carbohydrate complex / virus-host interaction
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Capsid protein VP1 / Capsid protein VP1
Similarity search - Component
Biological speciesMurine polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLiaci, A.M. / Buch, M.H.C. / Neu, U. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 685 Germany
CitationJournal: Plos Pathog. / Year: 2015
Title: Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity.
Authors: Buch, M.H. / Liaci, A.M. / O'Hara, S.D. / Garcea, R.L. / Neu, U. / Stehle, T.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,16619
Polymers158,1545
Non-polymers5,01314
Water33,2561846
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)220.450, 220.450, 99.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11E-762-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPVALVALAA44 - 4612 - 14
21ASPASPVALVALBB44 - 4612 - 14
31ASPASPVALVALCC44 - 4612 - 14
41ASPASPVALVALDD44 - 4612 - 14
51ASPASPVALVALEE44 - 4612 - 14
12GLUGLUILEILEAA48 - 4916 - 17
22GLUGLUILEILEBB48 - 4916 - 17
32GLUGLUILEILECC48 - 4916 - 17
42GLUGLUILEILEDD48 - 4916 - 17
52GLUGLUILEILEEE48 - 4916 - 17
13ALAALAALAALAAA5119
23ALAALAALAALABB5119
33ALAALAALAALACC5119
43ALAALAALAALADD5119
53ALAALAALAALAEE5119
14GLYGLYTHRTHRAA69 - 8337 - 51
24GLYGLYTHRTHRBB69 - 8337 - 51
34GLYGLYTHRTHRCC69 - 8337 - 51
44GLYGLYTHRTHRDD69 - 8337 - 51
54GLYGLYTHRTHREE69 - 8337 - 51
15ASPASPTHRTHRAA85 - 8653 - 54
25ASPASPTHRTHRBB85 - 8653 - 54
35ASPASPTHRTHRCC85 - 8653 - 54
45ASPASPTHRTHRDD85 - 8653 - 54
55ASPASPTHRTHREE85 - 8653 - 54
16ASPASPASPASPAA8856
26ASPASPASPASPBB8856
36ASPASPASPASPCC8856
46ASPASPASPASPDD8856
56ASPASPASPASPEE8856
17PROPROSERSERAA90 - 9958 - 67
27PROPROSERSERBB90 - 9958 - 67
37PROPROSERSERCC90 - 9958 - 67
47PROPROSERSERDD90 - 9958 - 67
57PROPROSERSEREE90 - 9958 - 67
18ALAALAASNASNAA101 - 10969 - 77
28ALAALAASNASNBB101 - 10969 - 77
38ALAALAASNASNCC101 - 10969 - 77
48ALAALAASNASNDD101 - 10969 - 77
58ALAALAASNASNEE101 - 10969 - 77
19GLNGLNASPASPAA118 - 14686 - 114
29GLNGLNASPASPBB118 - 14686 - 114
39GLNGLNASPASPCC118 - 14686 - 114
49GLNGLNASPASPDD118 - 14686 - 114
59GLNGLNASPASPEE118 - 14686 - 114
110VALVALTHRTHRAA190 - 192158 - 160
210VALVALTHRTHRBB190 - 192158 - 160
310VALVALTHRTHRCC190 - 192158 - 160
410VALVALTHRTHRDD190 - 192158 - 160
510VALVALTHRTHREE190 - 192158 - 160
111LYSLYSLYSLYSAA194162
211LYSLYSLYSLYSBB194162
311LYSLYSLYSLYSCC194162
411LYSLYSLYSLYSDD194162
511LYSLYSLYSLYSEE194162
112ILEILETHRTHRAA196 - 197164 - 165
212ILEILETHRTHRBB196 - 197164 - 165
312ILEILETHRTHRCC196 - 197164 - 165
412ILEILETHRTHRDD196 - 197164 - 165
512ILEILETHRTHREE196 - 197164 - 165
113LYSLYSLYSLYSAA199167
213LYSLYSLYSLYSBB199167
313LYSLYSLYSLYSCC199167
413LYSLYSLYSLYSDD199167
513LYSLYSLYSLYSEE199167
114ASNASNASNASNAA203171
214ASNASNASNASNBB203171
314ASNASNASNASNCC203171
414ASNASNASNASNDD203171
514ASNASNASNASNEE203171
115ASPASPGLNGLNAA205 - 206173 - 174
215ASPASPGLNGLNBB205 - 206173 - 174
315ASPASPGLNGLNCC205 - 206173 - 174
415ASPASPGLNGLNDD205 - 206173 - 174
515ASPASPGLNGLNEE205 - 206173 - 174
116LEULEUPROPROAA208 - 210176 - 178
216LEULEUPROPROBB208 - 210176 - 178
316LEULEUPROPROCC208 - 210176 - 178
416LEULEUPROPRODD208 - 210176 - 178
516LEULEUPROPROEE208 - 210176 - 178
117SERSERALAALAAA212 - 214180 - 182
217SERSERALAALABB212 - 214180 - 182
317SERSERALAALACC212 - 214180 - 182
417SERSERALAALADD212 - 214180 - 182
517SERSERALAALAEE212 - 214180 - 182
118LEULEUASPASPAA216 - 217184 - 185
218LEULEUASPASPBB216 - 217184 - 185
318LEULEUASPASPCC216 - 217184 - 185
418LEULEUASPASPDD216 - 217184 - 185
518LEULEUASPASPEE216 - 217184 - 185
119ASPASPGLYGLYAA219 - 220187 - 188
219ASPASPGLYGLYBB219 - 220187 - 188
319ASPASPGLYGLYCC219 - 220187 - 188
419ASPASPGLYGLYDD219 - 220187 - 188
519ASPASPGLYGLYEE219 - 220187 - 188
120TYRTYRTHRTHRAA222 - 237190 - 205
220TYRTYRTHRTHRBB222 - 237190 - 205
320TYRTYRTHRTHRCC222 - 237190 - 205
420TYRTYRTHRTHRDD222 - 237190 - 205
520TYRTYRTHRTHREE222 - 237190 - 205
121TYRTYRGLYGLYAA239 - 246207 - 214
221TYRTYRGLYGLYBB239 - 246207 - 214
321TYRTYRGLYGLYCC239 - 246207 - 214
421TYRTYRGLYGLYDD239 - 246207 - 214
521TYRTYRGLYGLYEE239 - 246207 - 214
122THRTHRPROPROAA248 - 251216 - 219
222THRTHRPROPROBB248 - 251216 - 219
322THRTHRPROPROCC248 - 251216 - 219
422THRTHRPROPRODD248 - 251216 - 219
522THRTHRPROPROEE248 - 251216 - 219
123LEULEULEULEUAA253221
223LEULEULEULEUBB253221
323LEULEULEULEUCC253221
423LEULEULEULEUDD253221
523LEULEULEULEUEE253221
124PHEPHETHRTHRAA255 - 258223 - 226
224PHEPHETHRTHRBB255 - 258223 - 226
324PHEPHETHRTHRCC255 - 258223 - 226
424PHEPHETHRTHRDD255 - 258223 - 226
524PHEPHETHRTHREE255 - 258223 - 226
125THRTHRTRPTRPAA260 - 288228 - 256
225THRTHRTRPTRPBB260 - 288228 - 256
325THRTHRTRPTRPCC260 - 288228 - 256
425THRTHRTRPTRPDD260 - 288228 - 256
525THRTHRTRPTRPEE260 - 288228 - 256
126THRTHRARGARGAA291 - 292259 - 260
226THRTHRARGARGBB291 - 292259 - 260
326THRTHRARGARGCC291 - 292259 - 260
426THRTHRARGARGDD291 - 292259 - 260
526THRTHRARGARGEE291 - 292259 - 260
127ASPASPASPASPAA295263
227ASPASPASPASPBB295263
327ASPASPASPASPCC295263
427ASPASPASPASPDD295263
527ASPASPASPASPEE295263
128HISHISLYSLYSAA297 - 312265 - 280
228HISHISLYSLYSBB297 - 312265 - 280
328HISHISLYSLYSCC297 - 312265 - 280
428HISHISLYSLYSDD297 - 312265 - 280
528HISHISLYSLYSEE297 - 312265 - 280

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.30634, 0.457722, 0.834654), (-0.456072, 0.840197, -0.293372), (-0.835556, -0.290791, 0.46614)35.453129, 51.320251, 93.864082
3given(-0.811927, 0.283174, 0.510477), (-0.277264, 0.582467, -0.764105), (-0.513711, -0.761935, -0.394407)148.028915, 50.671341, 93.119499
4given(-0.809425, -0.280375, -0.515966), (0.286649, 0.578205, -0.763879), (0.512506, -0.766204, -0.387645)182.099976, -0.76467, -0.37349
5given(0.310691, -0.457686, -0.833063), (0.457765, 0.840151, -0.290857), (0.83302, -0.290981, 0.47054)90.49884, -32.080959, -58.346371

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Components

#1: Protein
VP1


Mass: 31630.723 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine polyomavirus / Strain: PTA / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76TX8, UniProt: P49302*PLUS
#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2112h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-3/a4-b1_b3-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1846 / Source method: isolated from a natural source / Formula: H2O

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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: 4.42 Å3/Da / Density % sol: 72.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 1 M sodium phosphate, monobasic, 0.8 M potassium phosphate, dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 15, 2012
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 199442 / % possible obs: 96 % / Redundancy: 5.4 % / Rsym value: 0.113 / Net I/σ(I): 12.8
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.688 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CPU

5cpu


Resolution: 1.93→47.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.458 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 5954 3 %RANDOM
Rwork0.1531 ---
obs0.1537 192327 95.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.38 Å2 / Biso mean: 23.15 Å2 / Biso min: 10.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å20 Å2
2--0.03 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.93→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10880 0 323 1846 13049
Biso mean--36.61 31.13 -
Num. residues----1395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211788
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.99616157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63851467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5424.819496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.286151916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1951556
X-RAY DIFFRACTIONr_chiral_restr0.0670.21872
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218819
Refine LS restraints NCS

Ens-ID: 1 / Number: 1318 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.175
2BLOOSE POSITIONAL0.125
3CLOOSE POSITIONAL0.125
4DLOOSE POSITIONAL0.175
5ELOOSE POSITIONAL0.145
1ALOOSE THERMAL1.7910
2BLOOSE THERMAL1.4410
3CLOOSE THERMAL1.5310
4DLOOSE THERMAL1.7110
5ELOOSE THERMAL1.6710
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 413 -
Rwork0.208 13432 -
all-13845 -
obs--90.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0762-1.92731.37528.2836-3.57032.01820.001-0.0286-0.03630.25820.03330.0717-0.0824-0.0314-0.03420.2135-0.00570.04210.09830.00460.093197.48923.91352.602
21.0391-0.0316-0.10290.6359-0.04860.54560.0131-0.06330.02470.0824-0.01070.0235-0.05960.0032-0.00230.062-0.01560.0010.0084-0.00170.0021102.83945.94732.612
30.9511-0.52240.46013.229-2.22282.58810.0285-0.0482-0.08370.0748-0.0390.00820.03680.02470.01050.0245-0.01660.01270.0168-0.00840.022898.48337.1537.808
40.4226-0.2380.47153.1841-1.91241.92990.0396-0.1845-0.13980.08190.17120.34240.1462-0.2395-0.21080.1110.00010.04380.1720.02730.172663.85430.00434.887
50.56740.0840.19540.59230.0680.94170.0286-0.06920.02120.06230.00480.1015-0.011-0.1024-0.03340.03350.01520.0340.0511-0.00180.082273.80841.89930.117
60.56160.0349-0.29210.4481-0.08040.7505-0.00560.0155-0.0386-0.050.01460.14580.0799-0.1361-0.00910.0527-0.0041-0.02930.05580.00260.094868.18928.4194.806
71.05430.9423-0.56923.919-1.45851.3464-0.0156-0.0402-0.0637-0.00810.03110.12460.1078-0.0853-0.01550.02720.0062-0.01870.0433-0.01760.049171.10320.9016.803
80.78630.0553-0.03771.1097-0.41610.7506-0.00120.0555-0.1224-0.1795-0.0525-0.11720.12160.04920.05370.10580.01020.00140.0287-0.01760.045498.80718.663-10.101
90.46830.18560.05540.93710.04490.30960.01310.0052-0.0352-0.0321-0.01420.02140.0426-0.02820.0010.05540.0053-0.00040.0097-0.0070.012193.26319.845-4.187
100.24080.5283-0.12864.178-0.74390.92020.0373-0.0606-0.1490.2848-0.1161-0.4220.06670.13660.07880.0670.004-0.0380.0640.01950.1046121.95727.76122.042
110.42-0.0955-0.01061.01630.17090.79070.00540.0136-0.04760.0099-0.0219-0.07670.06390.07110.01640.0148-0.0013-0.00540.01380.00750.0236114.16930.4510.761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 52
2X-RAY DIFFRACTION2A53 - 258
3X-RAY DIFFRACTION3A259 - 316
4X-RAY DIFFRACTION4B35 - 65
5X-RAY DIFFRACTION5B66 - 316
6X-RAY DIFFRACTION6C35 - 258
7X-RAY DIFFRACTION7C259 - 316
8X-RAY DIFFRACTION8D34 - 108
9X-RAY DIFFRACTION9D109 - 316
10X-RAY DIFFRACTION10E35 - 71
11X-RAY DIFFRACTION11E72 - 316

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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

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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

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