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- PDB-4l63: Apo form of AB5 holotoxin -

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Basic information

Entry
Database: PDB / ID: 4l63
TitleApo form of AB5 holotoxin
Components
  • ECXA
  • ECXB
KeywordsHYDROLASE / MATRIX METALLOPROTEASE / AB5 TOXIN / OB FOLD / CHOLERA-LIKE TOXIN / PENTAMER / TOXIN / PROTEASE / GM1 / TOXILYSIN
Function / homology
Function and homology information


metallopeptidase activity / extracellular region / metal ion binding
Similarity search - Function
Met-zincin / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel ...Met-zincin / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLittler, D.R. / Ng, N.M. / Rossjohn, J. / Beddoe, T.
CitationJournal: Structure / Year: 2013
Title: EcxAB Is a Founding Member of a New Family of Metalloprotease AB5 Toxins with a Hybrid Cholera-like B Subunit.
Authors: Ng, N.M. / Littler, D.R. / Paton, A.W. / Le Nours, J. / Rossjohn, J. / Paton, J.C. / Beddoe, T.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: ECXA
B: ECXB
C: ECXB
D: ECXB
E: ECXB
F: ECXB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,62712
Polymers93,3706
Non-polymers1,2576
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15970 Å2
ΔGint-101 kcal/mol
Surface area30210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.530, 120.530, 273.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ECXA


Mass: 29492.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 176 / Gene: ecxA / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q8GAV4, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein
ECXB


Mass: 12775.468 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 176 / Gene: ecxB / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8GAV3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M HEPES and 0.6M Na/K/PO4, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953699 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: 2011 / Details: MONOCHROMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953699 Å / Relative weight: 1
ReflectionResolution: 1.8→39.5 Å / Num. obs: 109241 / % possible obs: 99.9 % / Observed criterion σ(I): 1.4 / Redundancy: 11.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WV6
Resolution: 1.8→45.211 Å / SU ML: 0.19 / Isotropic thermal model: ISOTROPIC / σ(F): 1.33 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 5289 5.02 %
Rwork0.1771 --
obs0.1781 105445 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 76 435 6547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076251
X-RAY DIFFRACTIONf_angle_d1.0938450
X-RAY DIFFRACTIONf_dihedral_angle_d15.2682373
X-RAY DIFFRACTIONf_chiral_restr0.048953
X-RAY DIFFRACTIONf_plane_restr0.0061077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.34041600.29643323X-RAY DIFFRACTION99
1.8205-1.84190.30071790.27723350X-RAY DIFFRACTION99
1.8419-1.86430.29251790.25973329X-RAY DIFFRACTION98
1.8643-1.88790.26712000.25033319X-RAY DIFFRACTION98
1.8879-1.91280.2791680.23583365X-RAY DIFFRACTION98
1.9128-1.9390.23441910.21583318X-RAY DIFFRACTION98
1.939-1.96670.23821530.21063360X-RAY DIFFRACTION98
1.9667-1.9960.22071750.20983322X-RAY DIFFRACTION98
1.996-2.02720.22791750.21693334X-RAY DIFFRACTION98
2.0272-2.06050.21231820.2013350X-RAY DIFFRACTION98
2.0605-2.0960.21531730.18213337X-RAY DIFFRACTION98
2.096-2.13410.20341860.18353306X-RAY DIFFRACTION98
2.1341-2.17520.21081830.17973334X-RAY DIFFRACTION98
2.1752-2.21960.1981600.17553351X-RAY DIFFRACTION98
2.2196-2.26780.20121640.17423356X-RAY DIFFRACTION98
2.2678-2.32060.20011710.1733352X-RAY DIFFRACTION97
2.3206-2.37860.18571690.17473316X-RAY DIFFRACTION97
2.3786-2.44290.19361900.16913320X-RAY DIFFRACTION97
2.4429-2.51480.19531830.17823341X-RAY DIFFRACTION97
2.5148-2.59590.21281760.17743302X-RAY DIFFRACTION97
2.5959-2.68870.20321750.18153354X-RAY DIFFRACTION97
2.6887-2.79640.21341840.18163319X-RAY DIFFRACTION96
2.7964-2.92360.21111740.18033319X-RAY DIFFRACTION96
2.9236-3.07770.20691760.18673335X-RAY DIFFRACTION96
3.0777-3.27050.19711680.17883320X-RAY DIFFRACTION95
3.2705-3.52290.18011590.16183320X-RAY DIFFRACTION95
3.5229-3.87730.16041940.15133329X-RAY DIFFRACTION95
3.8773-4.43790.15541790.14073333X-RAY DIFFRACTION94
4.4379-5.58960.17531730.14513378X-RAY DIFFRACTION94
5.5896-45.22560.20161900.19423464X-RAY DIFFRACTION91
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)
11.53920.27910.23933.4038-0.2083.05720.13490.2812-0.5648-0.22040.19690.22291.30220.39540.31330.80580.2343-0.21360.4727-0.14820.456919.868221.9225.0933
20.7682-0.55330.56550.4242-0.60381.5447-0.1769-0.5279-0.9675-0.03950.75380.48921.0889-0.7696-0.17121.2615-0.2639-0.25820.79390.30781.52237.07427.245419.4874
31.8570.2568-0.24731.48131.18061.05470.4390.0231-1.1176-0.18470.11920.31141.66520.21010.18671.40130.095-0.27830.4838-0.06690.974318.4239.751310.8908
41.9722-0.71510.39163.8073.0973.02740.0168-0.6449-0.80130.18040.62890.39270.9928-0.00770.08241.26430.0881-0.14040.89480.25160.682815.257612.572926.0463
52.66331.90214.54024.42671.29218.9807-0.2293-0.6925-0.23210.29380.39471.0299-0.1723-0.372-0.23380.9436-0.04180.35541.5110.59341.07331.227324.866729.83
63.6004-0.89430.70883.0329-0.96243.23010.1417-0.4675-0.71130.37860.28410.40390.7511-0.2478-0.13470.57360.0551-0.06290.42860.04020.48714.695124.913714.3876
78.3475-1.0736-1.44314.42840.20994.45410.009-0.283-0.60560.040.33741.02180.9408-0.5435-0.01350.5376-0.0744-0.09910.45840.07440.63388.64224.78047.7571
85.0968-1.9739-0.44515.3919-0.54814.37680.01410.3161-0.15640.00430.1577-0.39860.37560.3577-0.05240.31460.0303-0.06650.4748-0.12450.344618.548635.6968-3.5661
96.7821-2.73550.7831.1848-0.43990.2761-0.01540.3284-0.072-0.14220.08590.2257-0.0634-0.17390.27820.0941-0.1973-0.13771.05120.04140.3421-14.774949.2094-13.5328
100.66890.5992-0.20881.84720.83150.8585-0.02590.63720.1171-0.5522-0.10390.4257-0.085-0.4636-0.00340.3517-0.1958-0.22311.1101-0.0260.2638-10.957244.6279-22.9864
118.50544.1829-3.52542.7712-2.16252.05170.1423-0.2551-0.6544-0.0365-0.2230.08270.3046-0.02440.09070.3392-0.1752-0.01620.6384-0.24470.36460.570933.2974-15.8285
122.1975-0.2988-0.08480.23460.31421.2504-0.07281.17040.102-0.38520.10930.14210.0321-0.2226-0.14850.2943-0.1904-0.06550.8308-0.11290.22125.608746.3881-24.8724
133.9872-1.34190.11312.3366-0.77461.44890.00750.66210.323-0.09120.14520.0544-0.2032-0.2092-0.00290.1009-0.1036-0.09530.6114-0.0960.13865.231749.8183-14.8699
142.8345-0.01480.64240.18620.22670.8921-0.28510.8788-0.0319-0.21060.17510.03130.0234-0.1511-0.8030.2472-0.232-0.07520.8977-0.08560.2441-3.626242.021-21.2427
150.2002-0.52650.08441.52280.21111.7605-0.06520.2658-0.28560.03430.17320.31510.2803-0.1764-0.23780.1694-0.0675-0.04450.5689-0.05490.2684-4.147741.6456-11.8193
160.00620.10640.05734.02281.11660.6691-0.113-0.11760.69060.00240.02650.54750.0833-0.18580.02710.20610.043-0.02030.4317-0.10720.3818-2.713162.75314.2992
172.36870.8818-0.24531.1827-0.5291.503-0.109-0.24180.48510.0622-0.01620.2263-0.2521-0.5384-0.26320.08230.1003-0.04350.5464-0.10330.3838-11.365458.30738.801
184.2193-0.2307-1.19873.29383.17625.32920.1231-0.4353-0.3030.3631-0.10060.06850.466-0.0670.15520.1521-0.00680.00940.4068-0.03790.3046-5.316142.33165.5458
191.1452-0.15670.28010.78560.6690.9373-0.11980.34310.3097-0.27220.10770.1925-0.2165-0.2298-0.11770.1175-0.004-0.05130.50190.02960.2993-7.486353.1345-6.8022
201.9726-0.8448-0.05585.41490.71760.949100.40650.1897-0.21130.02580.0346-0.0919-0.03250.00580.0927-0.0193-0.04220.4174-0.04290.19772.43554.6498-3.5653
212.33930.14650.34181.2870.25590.9988-0.11670.09230.18560.1381-0.00830.03510.071-0.1572-0.00350.10150.0076-0.01030.3972-0.04030.2315-5.906752.43535.3966
222.62062.142-0.27932.2582-0.28770.2363-0.00730.15050.12390.13240.3261-0.2982-0.11760.41540.20310.18230.0078-0.06790.4317-0.1260.310630.141163.901611.3262
234.69810.0304-0.57362.4033-2.30066.23080.2383-0.18570.47750.7824-0.0993-0.0499-0.55060.22740.18520.2185-0.0183-0.04270.2502-0.1170.201520.962965.474517.483
245.17760.83795.62933.32420.43376.23450.1936-0.3701-0.51220.51650.0871-0.27910.31610.146-0.16650.18940.0319-0.06240.2758-0.0660.177914.58648.784416.4039
252.13520.5534-0.1630.76030.32160.5889-0.00430.16320.39280.0330.03530.1774-0.1029-0.0329-0.06750.1360.0258-0.03850.2613-0.0520.24456.848561.7299.408
262.90322.8058-0.69015.4995-0.69050.8003-0.12610.25370.2739-0.06120.1123-0.0741-0.1145-0.0297-0.05810.10770.01-0.03830.3101-0.04860.198113.284258.00921.9229
272.12931.01780.58042.30040.6841.7897-0.022-0.040.29520.2901-0.00640.0585-0.0506-0.05920.06250.15770.0255-0.05310.2501-0.08010.194115.759959.877914.8586
280.97670.23690.50590.2525-0.60563.2594-0.0215-0.0191-0.14110.2349-0.0598-0.28670.36280.19060.09040.14230.0164-0.05350.2594-0.07450.244821.513854.156811.1196
291.16251.032-0.3913.4971-1.78261.0715-0.33860.5129-0.0676-0.4197-0.0986-0.2186-0.05810.2713-0.13550.2303-0.04440.05340.6509-0.04890.343638.474351.0779-17.0503
305.5806-1.05811.70571.84510.07112.3934-0.30830.54170.4732-0.1028-0.0712-0.2051-0.30090.37010.02170.1341-0.0583-0.00560.608-0.00470.294441.600555.4649-7.8225
314.3728-4.8085-4.42616.75414.21735.4292-0.273-0.0372-0.76660.06910.0198-0.16730.40470.60630.09730.11740.0544-0.01210.3908-0.0460.3632.678243.8272.2592
321.8310.2878-0.77340.90990.78841.2438-0.01060.26960.26790.10850.051-0.3976-0.16090.26670.210.1224-0.0165-0.04580.3529-0.04140.300928.527859.7041.6388
332.42171.6381-1.77823.1964-2.16933.6917-0.12190.49170.2869-0.1350.14680.0229-0.0383-0.1904-0.16330.1137-0.0141-0.02550.4126-0.04850.275522.740955.2355-5.9844
345.69584.551-5.94015.5132-3.26277.3729-0.0051-0.0161-0.36390.1058-0.1914-0.14580.22430.04090.07440.1605-0.03230.03880.4055-0.12410.347429.758742.2657-2.0541
353.91230.8060.04191.56860.15841.734-0.13920.050.4627-0.02080.00140.0179-0.07690.2324-0.14490.0818-0.0323-0.0280.4563-0.02440.338737.839757.8292-3.464
363.2367-2.6935-1.69222.61470.93272.6-0.13880.1779-0.52310.0214-0.16140.03060.26220.1923-0.19590.0860.0080.01930.4545-0.05360.286832.004146.4909-7.766
370.8943-0.0578-0.38552.4306-0.81953.4661-0.04120.714-0.0385-0.4962-0.17020.30220.2042-0.110.06860.4883-0.2003-0.0061.0066-0.22320.29511.409342.0657-32.9956
382.8341-1.20680.8351.44560.76632.1722-0.03531.01510.0125-0.3297-0.1297-0.0690.01280.1439-0.26080.4256-0.11450.13791.0381-0.22480.210621.905242.7761-33.1172
393.89094.28373.59296.63164.47446.08630.10.3566-0.7093-0.0503-0.194-0.04581.03380.181-0.11850.40810.04890.07860.5778-0.29490.496124.277534.2051-17.9169
402.46811.03510.35131.34170.05072.49-0.10680.6779-0.1676-0.20890.0313-0.10790.01290.239-0.08530.1667-0.02050.05690.5876-0.0960.287329.456747.9726-17.566
412.1978-0.7871.0453.2123-2.173.6235-0.17360.69620.2386-0.34290.0428-0.2542-0.1123-0.00250.08280.1977-0.06510.00510.5857-0.05110.247919.095952.2274-18.8477
421.1574-0.33160.15120.54710.93763.928-0.06270.6743-0.1961-0.21650.0224-0.30530.21230.25390.10410.2753-0.10010.08930.8119-0.19590.30223.744942.3818-25.4193
431.7125-0.26820.57161.0967-0.29036.1189-0.03130.4059-0.2003-0.20830.02280.08120.5475-0.06810.06650.2173-0.1333-0.04990.815-0.2680.171816.636540.0118-22.5029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 133 )
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 164 )
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 234 )
7X-RAY DIFFRACTION7chain 'A' and (resid 235 through 258 )
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 278 )
9X-RAY DIFFRACTION9chain 'B' and (resid 0 through 11 )
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 19 )
11X-RAY DIFFRACTION11chain 'B' and (resid 20 through 25 )
12X-RAY DIFFRACTION12chain 'B' and (resid 26 through 58 )
13X-RAY DIFFRACTION13chain 'B' and (resid 59 through 78 )
14X-RAY DIFFRACTION14chain 'B' and (resid 79 through 94 )
15X-RAY DIFFRACTION15chain 'B' and (resid 95 through 104 )
16X-RAY DIFFRACTION16chain 'C' and (resid 0 through 11 )
17X-RAY DIFFRACTION17chain 'C' and (resid 12 through 19 )
18X-RAY DIFFRACTION18chain 'C' and (resid 20 through 25 )
19X-RAY DIFFRACTION19chain 'C' and (resid 26 through 58 )
20X-RAY DIFFRACTION20chain 'C' and (resid 59 through 78 )
21X-RAY DIFFRACTION21chain 'C' and (resid 79 through 104 )
22X-RAY DIFFRACTION22chain 'D' and (resid 0 through 11 )
23X-RAY DIFFRACTION23chain 'D' and (resid 12 through 19 )
24X-RAY DIFFRACTION24chain 'D' and (resid 20 through 25 )
25X-RAY DIFFRACTION25chain 'D' and (resid 26 through 58 )
26X-RAY DIFFRACTION26chain 'D' and (resid 59 through 78 )
27X-RAY DIFFRACTION27chain 'D' and (resid 79 through 94 )
28X-RAY DIFFRACTION28chain 'D' and (resid 95 through 104 )
29X-RAY DIFFRACTION29chain 'E' and (resid 1 through 11 )
30X-RAY DIFFRACTION30chain 'E' and (resid 12 through 19 )
31X-RAY DIFFRACTION31chain 'E' and (resid 20 through 25 )
32X-RAY DIFFRACTION32chain 'E' and (resid 26 through 58 )
33X-RAY DIFFRACTION33chain 'E' and (resid 59 through 78 )
34X-RAY DIFFRACTION34chain 'E' and (resid 79 through 83 )
35X-RAY DIFFRACTION35chain 'E' and (resid 84 through 94 )
36X-RAY DIFFRACTION36chain 'E' and (resid 95 through 104 )
37X-RAY DIFFRACTION37chain 'F' and (resid 1 through 11 )
38X-RAY DIFFRACTION38chain 'F' and (resid 12 through 19 )
39X-RAY DIFFRACTION39chain 'F' and (resid 20 through 25 )
40X-RAY DIFFRACTION40chain 'F' and (resid 26 through 50 )
41X-RAY DIFFRACTION41chain 'F' and (resid 51 through 78 )
42X-RAY DIFFRACTION42chain 'F' and (resid 79 through 94 )
43X-RAY DIFFRACTION43chain 'F' and (resid 95 through 103 )

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