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- PDB-7zaz: macrocyclase OphP with ZPP -

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Basic information

Entry
Database: PDB / ID: 7zaz
Titlemacrocyclase OphP with ZPP
ComponentsProlyl endopeptidase
KeywordsHYDROLASE / macrocyclase for omphalotin A biosynthesis
Function / homologyZ-PRO-PROLINAL / BICARBONATE ION / PHOSPHATE ION / N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL
Function and homology information
Biological speciesOmphalotus olearius (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSong, H. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R018189/1 United Kingdom
CitationJournal: Biorxiv / Year: 2022
Title: Molecular basis for the enzymatic macrocyclization of multiply backbone N-methylated peptides
Authors: Matabaro, E. / Song, H. / Gherlone, F. / Sonderegger, L. / Giltrap, A. / Liver, S. / Gossert, A. / Kunzler, M. / Naismith, J.H.
History
DepositionMar 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
AAA: Prolyl endopeptidase
BBB: Prolyl endopeptidase
CCC: Prolyl endopeptidase
DDD: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,74648
Polymers337,8464
Non-polymers3,90044
Water23,9241328
1
AAA: Prolyl endopeptidase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 85.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)85,56214
Polymers84,4621
Non-polymers1,10013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Prolyl endopeptidase
hetero molecules


  • defined by author
  • 85.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)85,35911
Polymers84,4621
Non-polymers89810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Prolyl endopeptidase
hetero molecules


  • defined by author
  • 85.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)85,31310
Polymers84,4621
Non-polymers8529
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Prolyl endopeptidase
hetero molecules


  • defined by author
  • 85.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)85,51213
Polymers84,4621
Non-polymers1,05112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.680, 102.650, 110.270
Angle α, β, γ (deg.)116.230, 101.090, 92.180
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYTHRTHRAAAA5 - 7315 - 731
211GLYGLYTHRTHRBBBB5 - 7315 - 731
322TRPTRPGLNGLNAAAA6 - 7306 - 730
422TRPTRPGLNGLNCCCC6 - 7306 - 730
533TRPTRPTHRTHRAAAA6 - 7316 - 731
633TRPTRPTHRTHRDDDD6 - 7316 - 731
744TRPTRPGLNGLNBBBB6 - 7306 - 730
844TRPTRPGLNGLNCCCC6 - 7306 - 730
955TRPTRPTHRTHRBBBB6 - 7316 - 731
1055TRPTRPTHRTHRDDDD6 - 7316 - 731
1166TRPTRPGLNGLNCCCC6 - 7306 - 730
1266TRPTRPGLNGLNDDDD6 - 7306 - 730

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Prolyl endopeptidase / macrocyclase / OphP


Mass: 84461.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115

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Non-polymers , 8 types, 1372 molecules

#2: Chemical
ChemComp-ZPR / N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL / Z-PRO-PROLINAL


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 330.378 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H22N2O4 / Feature type: SUBJECT OF INVESTIGATION / References: Z-PRO-PROLINAL
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical...
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1328 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M Bis-Tris propane (pH 6.0-6.5) and 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→67.799 Å / Num. obs: 175661 / % possible obs: 97.6 % / Redundancy: 3.5 % / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.136 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 1.099 / Num. unique obs: 8274 / CC1/2: 0.58 / Rrim(I) all: 1.308 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N4C
Resolution: 2→67.799 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 15.349 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / ESU R: 0.254 / ESU R Free: 0.192
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2452 8559 4.874 %
Rwork0.209 167043 -
all0.211 --
obs-175602 97.544 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.623 Å2-0.622 Å2-0.449 Å2
2---0.312 Å2-0.92 Å2
3---1.322 Å2
Refinement stepCycle: LAST / Resolution: 2→67.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22761 0 257 1328 24346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01323692
X-RAY DIFFRACTIONr_bond_other_d0.0010.01721321
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.65332090
X-RAY DIFFRACTIONr_angle_other_deg1.1841.58349232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89652837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.5521.9281302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.503153757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.39715149
X-RAY DIFFRACTIONr_chiral_restr0.0560.22947
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0226921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025725
X-RAY DIFFRACTIONr_nbd_refined0.1870.24192
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.220641
X-RAY DIFFRACTIONr_nbtor_refined0.1640.211228
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.210994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.21290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.287
X-RAY DIFFRACTIONr_nbd_other0.2320.2300
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.234
X-RAY DIFFRACTIONr_mcbond_it1.5631.96211369
X-RAY DIFFRACTIONr_mcbond_other1.5621.96211368
X-RAY DIFFRACTIONr_mcangle_it2.4742.93614199
X-RAY DIFFRACTIONr_mcangle_other2.4742.93714200
X-RAY DIFFRACTIONr_scbond_it2.0192.2212323
X-RAY DIFFRACTIONr_scbond_other2.0192.2212324
X-RAY DIFFRACTIONr_scangle_it3.1223.23717891
X-RAY DIFFRACTIONr_scangle_other3.1223.23717892
X-RAY DIFFRACTIONr_lrange_it5.74123.36825991
X-RAY DIFFRACTIONr_lrange_other5.74123.36925992
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.0523084
X-RAY DIFFRACTIONr_ncsr_local_group_20.0780.0522676
X-RAY DIFFRACTIONr_ncsr_local_group_30.0870.0523398
X-RAY DIFFRACTIONr_ncsr_local_group_40.0730.0522706
X-RAY DIFFRACTIONr_ncsr_local_group_50.0760.0523002
X-RAY DIFFRACTIONr_ncsr_local_group_60.0730.0522737
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.079330.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.079330.0501
23AAAX-RAY DIFFRACTIONLocal ncs0.077590.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.077590.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.086530.0501
36DDDX-RAY DIFFRACTIONLocal ncs0.086530.0501
47BBBX-RAY DIFFRACTIONLocal ncs0.072670.0501
48CCCX-RAY DIFFRACTIONLocal ncs0.072670.0501
59BBBX-RAY DIFFRACTIONLocal ncs0.075590.0501
510DDDX-RAY DIFFRACTIONLocal ncs0.075590.0501
611CCCX-RAY DIFFRACTIONLocal ncs0.073350.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.073350.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3296480.33411891X-RAY DIFFRACTION94.1578
2.052-2.1080.3656230.35211959X-RAY DIFFRACTION96.9786
2.108-2.1690.3055590.29111612X-RAY DIFFRACTION96.3887
2.169-2.2360.2965650.27611335X-RAY DIFFRACTION97.1508
2.236-2.3090.3265740.28710994X-RAY DIFFRACTION97.4558
2.309-2.390.2995400.24910715X-RAY DIFFRACTION97.5219
2.39-2.480.3045510.24110254X-RAY DIFFRACTION97.7563
2.48-2.5820.2715340.2299937X-RAY DIFFRACTION97.9056
2.582-2.6960.274630.2299533X-RAY DIFFRACTION97.9616
2.696-2.8280.2684600.219060X-RAY DIFFRACTION97.3216
2.828-2.9810.2564820.2058626X-RAY DIFFRACTION97.8829
2.981-3.1610.2314070.1978203X-RAY DIFFRACTION98.254
3.161-3.3790.2133700.1877791X-RAY DIFFRACTION98.6462
3.379-3.650.2263490.1857270X-RAY DIFFRACTION98.8582
3.65-3.9970.2163300.1766649X-RAY DIFFRACTION99.021
3.997-4.4680.1843040.1536054X-RAY DIFFRACTION99.1269
4.468-5.1580.1972580.1535349X-RAY DIFFRACTION99.0111
5.158-6.3120.2242620.1844458X-RAY DIFFRACTION98.7861
6.312-8.9080.2071690.1753468X-RAY DIFFRACTION98.9122
8.908-67.7990.1851110.1881886X-RAY DIFFRACTION98.0363
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.6146-1.34690.11587.65312.12723.11340.14220.0585-0.095-0.3218-0.21740.2919-0.097-0.34260.07520.0409-0.0444-0.01150.21440.01630.1901-2.7974-65.05150.2191
22.336-0.1340.93153.09761.14614.69260.06920.19490.3203-0.417-0.21490.0842-0.753-0.22460.14570.16420.03660.00980.19230.0010.26873.5796-51.693249.8692
33.443-0.8697-2.09170.66120.34891.35850.25110.17540.3206-0.0037-0.1041-0.0865-0.2063-0.0808-0.1470.1251-0.05210.00310.1073-0.06220.300134.8074-45.097360.2575
41.89790.5320.75921.61241.04071.9055-0.03130.03240.2098-0.1258-0.02670.0342-0.1303-0.07740.0580.0385-0.02960.03540.0545-0.02390.280438.7557-49.724543.2172
50.9564-0.048-0.19470.41080.09590.52850.0182-0.0333-0.03490.02390.0086-0.06790.00920.0245-0.02680.0141-0.0209-0.00110.0422-0.03850.246427.7896-67.122257.6367
63.28170.7766-2.9442.2448-2.30578.5508-0.04410.11160.0761-0.10980.1241-0.00210.11440.0617-0.080.1019-0.0482-0.00970.0626-0.01860.193416.9183-46.867963.7138
71.92810.29470.85840.27560.41544.83030.03270.26850.3132-0.10870.0734-0.0698-0.60230.4316-0.10620.1849-0.04920.04880.0683-0.01610.316734.0775-79.40893.8668
81.80230.2159-0.13331.85960.43742.29310.14510.18980.1747-0.0987-0.1437-0.08-0.2538-0.0538-0.00140.0730.0025-0.01220.2086-0.02540.315-4.4202-81.3106-0.4474
91.5729-0.33490.11192.2279-0.10450.76790.0114-0.00320.1297-0.0645-0.02940.0808-0.0244-0.16940.0180.0621-0.0580.02030.1173-0.0670.21512.2559-78.553524.7733
101.3519-0.37480.38830.8671-0.74393.74230.0767-0.0155-0.15130.0101-0.03580.09920.3005-0.2192-0.04090.1055-0.1069-0.00570.1231-0.05080.2935-5.1269-101.028412.0111
110.8277-0.0432-0.2671.04090.37531.25510.0220.08750.0289-0.0148-0.03220.03910.0182-0.06260.01030.009-0.00980.02230.0301-0.04460.224324.1116-98.78887.6273
121.5160.56330.98261.02860.65653.97790.02740.24840.2326-0.0667-0.01260.0562-0.2399-0.1116-0.01480.1017-0.01580.05670.10070.01530.245128.2795-85.88-1.4715
133.3954-0.8922-0.40740.57660.22520.1936-0.0199-0.6975-0.3260.05020.05350.12990.0421-0.0574-0.03360.1022-0.04180.01810.34970.02930.268725.6091-72.0262-32.7913
141.20430.1912-0.58641.20551.61983.2023-0.0509-0.173-0.07460.29710.0103-0.02630.3370.06870.04070.17740-0.03060.0717-0.01670.297758.3809-76.5743-25.9947
151.944-0.3188-0.06911.8501-0.22750.9971-0.0457-0.1780.07710.18960.0148-0.12040.06460.03960.03090.0385-0.02150.0080.0914-0.09310.256754.3183-53.9638-17.3971
161.4530.09940.39790.68720.35310.44220.00230.13870.0748-0.0947-0.019-0.0585-0.05930.01460.01670.0375-0.03620.03070.0881-0.03570.220452.783-59.8238-46.1063
173.10870.3748-0.24631.90920.18351.39560.0618-0.27560.21720.0053-0.10210.067-0.0619-0.11570.04040.0079-0.0129-0.00950.1229-0.07780.219428.4664-56.4325-41.1655
183.1959-1.305-0.32141.40230.20270.4246-0.0694-0.5054-0.37070.14890.10190.02790.03510.0272-0.03250.0349-0.0460.01240.2052-0.00570.280824.23-71.4047-38.5976
191.1077-0.35410.23791.0236-0.75184.23970.0779-0.0185-0.2017-0.1081-0.02160.00360.43960.3346-0.05630.06590.0091-0.01440.0897-0.07460.229255.6806-43.03646.0536
202.76630.2770.66540.2629-0.23810.93270.1477-0.2195-0.24720.0852-0.0746-0.04790.1359-0.0038-0.07310.1342-0.0584-0.00590.0847-0.06970.274326.8839-36.438125.8991
216.1763-2.55610.19932.86030.41542.3766-0.0677-0.2326-0.21510.21990.12740.01110.1275-0.0234-0.05970.1109-0.0652-0.00750.06660.01550.137813.7121-43.817522.831
222.16770.5142-2.21570.8567-0.50222.78320.0115-0.064-0.1490.10840.002-0.09410.15250.0829-0.01360.1073-0.0358-0.02940.0491-0.05410.272518.9851-54.72465.8817
231.54180.20240.50272.2503-0.05251.09750.01060.1804-0.2062-0.16290.00960.08350.1004-0.134-0.02020.0359-0.0404-0.00060.1058-0.0740.21515.8796-41.9689-10.92
240.88970.04740.09590.30780.01990.45830.0166-0.0781-0.01690.0248-0.00180.02760.0121-0.0081-0.01480.0199-0.02340.01080.0441-0.05310.210431.2821-26.25128.825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA5 - 29
2X-RAY DIFFRACTION2ALLAAA30 - 68
3X-RAY DIFFRACTION3ALLAAA69 - 111
4X-RAY DIFFRACTION4ALLAAA112 - 228
5X-RAY DIFFRACTION5ALLAAA229 - 697
6X-RAY DIFFRACTION6ALLAAA698 - 731
7X-RAY DIFFRACTION7ALLBBB5 - 77
8X-RAY DIFFRACTION8ALLBBB78 - 164
9X-RAY DIFFRACTION9ALLBBB165 - 347
10X-RAY DIFFRACTION10ALLBBB348 - 456
11X-RAY DIFFRACTION11ALLBBB457 - 651
12X-RAY DIFFRACTION12ALLBBB652 - 731
13X-RAY DIFFRACTION13ALLCCC6 - 92
14X-RAY DIFFRACTION14ALLCCC93 - 205
15X-RAY DIFFRACTION15ALLCCC206 - 330
16X-RAY DIFFRACTION16ALLCCC331 - 538
17X-RAY DIFFRACTION17ALLCCC539 - 641
18X-RAY DIFFRACTION18ALLCCC642 - 730
19X-RAY DIFFRACTION19ALLDDD6 - 56
20X-RAY DIFFRACTION20ALLDDD57 - 106
21X-RAY DIFFRACTION21ALLDDD107 - 149
22X-RAY DIFFRACTION22ALLDDD150 - 262
23X-RAY DIFFRACTION23ALLDDD263 - 336
24X-RAY DIFFRACTION24ALLDDD337 - 731

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