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- PDB-4koe: Quinolone(Trovafloxacin)-DNA cleavage complex of type IV topoisom... -

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Basic information

Entry
Database: PDB / ID: 4koe
TitleQuinolone(Trovafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae
Components
  • (DNA topoisomerase 4 subunit ...) x 2
  • E-site DNA1
  • E-site DNA2
  • E-site DNA3
  • E-site DNA4
KeywordsISOMERASE/DNA/INHIBITOR / PROTEIN-DNA CLEAVAGE COMPLEX / ISOMERASE-DNA-INHIBITOR COMPLEX / TOPOISOMERASE IIA / Quinolone / Trovafloxacin
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / Rossmann fold - #670 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A ...DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / Rossmann fold - #670 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Trovafloxacin / DNA / DNA (> 10) / DNA topoisomerase 4 subunit A / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Streptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsLaponogov, I. / Pan, X.-S. / Veselkov, D.A. / Fisher, L.M. / Sanderson, M.R.
CitationJournal: To be Published
Title: Inhibitor-stabilised cleavage complexes of topoisomerase IIa: structural analysis of drug-dependent inter- and intramolecular interactions
Authors: Laponogov, I. / Pan, X.-S. / Veselkov, D.A. / Fisher, L.M. / Sanderson, M.R.
History
DepositionMay 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 4 subunit A
B: DNA topoisomerase 4 subunit A
C: DNA topoisomerase 4 subunit B
D: DNA topoisomerase 4 subunit B
E: E-site DNA1
F: E-site DNA2
G: E-site DNA3
H: E-site DNA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,66216
Polymers184,6848
Non-polymers9798
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.040, 158.040, 210.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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DNA topoisomerase 4 subunit ... , 2 types, 4 molecules ABCD

#1: Protein DNA topoisomerase 4 subunit A / Topoisomerase IV subunit A


Mass: 56455.434 Da / Num. of mol.: 2 / Fragment: ParC55, UNP residues 1-488 / Mutation: I257T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: parC, SP_0855 / Production host: Escherichia coli (E. coli) / References: UniProt: P72525, EC: 5.99.1.3
#2: Protein DNA topoisomerase 4 subunit B


Mass: 30415.703 Da / Num. of mol.: 2 / Fragment: ParE30, UNP residues 404-647 / Mutation: V460I, T644A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: parE / Production host: Escherichia coli (E. coli) / References: UniProt: Q59961, EC: 5.99.1.3

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DNA chain , 4 types, 4 molecules EFGH

#3: DNA chain E-site DNA1


Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: E-site DNA
#4: DNA chain E-site DNA2


Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: E-site DNA
#5: DNA chain E-site DNA3


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: E-site DNA
#6: DNA chain E-site DNA4


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: E-site DNA

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Non-polymers , 2 types, 8 molecules

#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-TR6 / Trovafloxacin / 7-[(1R,5S,6s)-6-amino-3-azabicyclo[3.1.0]hex-3-yl]-1-(2,4-difluorophenyl)-6-fluoro-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid


Mass: 416.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H15F3N4O3 / Comment: antibiotic*YM

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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: 4.11 Å3/Da / Density % sol: 70.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM Na Cacodylate, 4-7% isopropanol, optimized mixture of salts, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2012
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.02→62.42 Å / Num. all: 60269 / Num. obs: 60245 / % possible obs: 99.96 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 19.59 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.14
Reflection shellResolution: 3.02→3.12 Å / Redundancy: 20.48 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.96 / % possible all: 99.91

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Processing

Software
NameVersionClassification
GDEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
xia2data reduction
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→62.42 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 3024 5.03 %RANDOM
Rwork0.1753 ---
obs0.1771 60105 99.93 %-
all-60147 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.715 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9238 Å20 Å2-0 Å2
2--4.9238 Å2-0 Å2
3----9.8477 Å2
Refinement stepCycle: LAST / Resolution: 3.02→62.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10309 730 66 0 11105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811379
X-RAY DIFFRACTIONf_angle_d1.20115619
X-RAY DIFFRACTIONf_dihedral_angle_d17.194141
X-RAY DIFFRACTIONf_chiral_restr0.0771791
X-RAY DIFFRACTIONf_plane_restr0.0051911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0201-3.06730.30891310.27112571X-RAY DIFFRACTION100
3.0673-3.11760.28431330.23362574X-RAY DIFFRACTION100
3.1176-3.17130.32421310.22442573X-RAY DIFFRACTION100
3.1713-3.2290.24671510.21072532X-RAY DIFFRACTION100
3.229-3.29110.24841330.20182598X-RAY DIFFRACTION100
3.2911-3.35830.23941260.20392543X-RAY DIFFRACTION100
3.3583-3.43130.25221370.20112590X-RAY DIFFRACTION100
3.4313-3.51110.23271530.19442569X-RAY DIFFRACTION100
3.5111-3.59890.25461210.1892570X-RAY DIFFRACTION100
3.5989-3.69620.25751360.18182558X-RAY DIFFRACTION100
3.6962-3.80490.20491570.17572555X-RAY DIFFRACTION100
3.8049-3.92770.22211550.16412564X-RAY DIFFRACTION100
3.9277-4.06810.20911330.16072586X-RAY DIFFRACTION100
4.0681-4.23090.2041350.14652579X-RAY DIFFRACTION100
4.2309-4.42340.16581480.13762575X-RAY DIFFRACTION100
4.4234-4.65660.16271390.12862590X-RAY DIFFRACTION100
4.6566-4.94820.15921360.13632622X-RAY DIFFRACTION100
4.9482-5.33010.20931480.16152588X-RAY DIFFRACTION100
5.3301-5.86610.26051390.18522632X-RAY DIFFRACTION100
5.8661-6.71410.23421320.20662624X-RAY DIFFRACTION100
6.7141-8.45570.17551210.16362697X-RAY DIFFRACTION100
8.4557-62.4340.17021290.192791X-RAY DIFFRACTION100
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)
10.37940.5131-0.45069.1824-7.53876.1105-0.0924-0.0645-0.00480.313-0.1611-0.6556-0.09140.22410.16950.4973-0.01830.00550.5376-0.06330.2632-79.604739.585244.4423
22.60550.4277-0.2816.0217-0.61025.91960.2218-0.16070.09370.2126-0.1858-0.6193-0.12210.4696-0.02860.31070.0118-0.01070.52610.00310.3296-72.505462.09227.3551
36.597-2.8586-0.32297.1512-2.3778.80150.49371.4727-0.4277-0.47140.06370.6252-0.88840.2485-0.58590.71930.3158-0.09630.9051-0.13560.4649-68.92286.835839.3903
41.215-0.1091-1.22581.0657-1.16272.7112-0.04990.34080.2196-0.0276-0.3684-0.0989-0.10161.31880.3540.63690.2066-0.30951.5858-0.45061.2403-52.1355-1.858835.7422
52.82981.21710.17843.59520.4413.2214-0.10590.3203-0.0566-0.41640.23850.0295-0.02360.1244-0.12530.64910.02420.03030.37980.01290.2656-84.96615.820731.117
63.3373-3.37361.28322.1762-5.52835.45050.01690.5096-0.03120.53740.11750.0817-0.57080.03950.00090.8-0.0856-0.04970.6498-0.11420.3185-85.275251.702144.3111
74.4142-0.15450.80046.49361.40213.30930.2236-0.211-0.20070.1531-0.02910.78220.3658-0.5624-0.13320.6793-0.16050.03360.57530.09480.445-105.1521-12.367743.4214
83.65093.42411.30198.06732.73032.48520.17840.28160.35740.3589-0.17710.4713-0.1606-0.13060.12840.6930.0940.06580.433-0.03120.3042-93.583324.586751.935
91.71420.350.26942.8550.31381.83170.0665-0.4156-0.19580.7463-0.02360.06480.49760.2769-0.04290.78770.06340.00120.49820.01670.3221-86.92379.198753.8117
100.19370.61450.4177.43834.9774.004-0.11490.05270.0945-0.029-0.16580.57040.2107-0.24220.19380.4930.04160.02680.55270.05520.2852-80.780242.0537-5.6273
112.57631.33932.03356.7624-0.25126.89340.11510.0480.08470.3488-0.01540.4204-0.3476-0.505-0.04330.33990.11770.0580.5437-0.02440.2816-83.475164.130213.7539
122.01760.04721.5588.8662-0.48847.52220.2149-2.1046-0.45611.00090.4427-0.4946-0.8725-0.8963-0.36450.6928-0.1407-0.14110.85840.11520.4076-94.4799.6632-3.4859
137.9463-0.1444-3.31225.4289-0.23548.8048-0.148-0.2019-0.7073-0.2650.46170.6470.2027-1.9996-0.39550.6405-0.0131-0.12131.00990.25651.0196-111.86382.1904-0.2378
142.7276-0.29670.23954.0752-1.38653.6761-0.1155-0.32950.01840.54220.22490.1309-0.2915-0.07-0.09540.60770.050.06970.4083-0.01220.2631-77.925916.85965.5384
154.61013.41621.85542.32885.19146.3072-0.0212-0.01060.1456-0.06370.58480.0211-0.22020.3847-0.44090.66470.1224-0.01270.47680.03370.3479-73.669553.0021-4.4787
165.8658-0.28171.33795.5618-0.52944.22140.13530.0812-0.1070.11070.1507-0.57470.20390.6025-0.27920.49890.0280.05180.4464-0.07620.395-58.901-11.0034-9.3491
172.7684-2.54650.47465.1554-1.3761.7776-0.11230.2662-0.03990.0047-0.2021-0.2103-0.23050.0620.32860.6619-0.07430.08220.4995-0.02510.2733-68.640326.5442-14.1256
180.98580.0684-0.04631.82110.46851.55030.09820.3258-0.1087-0.58840.106-0.04930.2508-0.1693-0.14990.7954-0.00970.01630.5497-0.01590.305-76.425112.2421-17.3803
192.9735.3269-3.64632.0381-5.99292.01230.2714-1.20652.01351.60650.901-1.0295-0.47591.5597-1.21240.85890.0707-0.12661.0217-0.4421.4279-53.693614.870923.1428
201.8320.43160.45154.15460.31033.3209-0.3421-0.6576-0.35830.70520.3313-0.43530.58770.6273-0.08060.9920.4386-0.23451.20650.01950.6497-60.3807-6.17246.6775
211.5640.1457-0.88820.82450.40682.2507-0.3005-0.0381-0.1020.04480.3489-0.46630.51010.6598-0.01350.86080.4023-0.07330.9968-0.20380.6695-57.9967-7.799524.0825
226.6473-5.8302-1.42846.85551.85285.7243-0.2122-0.89810.78530.14491.23570.9733-0.3896-1.0066-0.98360.96050.01620.22121.12150.20841.236-109.431517.221413.5869
237.9944-0.3915-0.04216.87972.94985.9668-0.15921.3386-0.241-1.05760.71870.93150.4093-0.8449-0.43861.0116-0.3498-0.26151.09860.13480.6597-104.3714-2.0263-11.762
243.3132-0.0687-0.85892.1546-1.09032.7448-0.2164-0.1725-0.56860.11660.37080.63160.59-0.7997-0.10640.7948-0.2983-0.03150.93170.24590.8133-106.2951-5.555410.4185
254.5216-1.55681.52474.4863-0.02717.7950.58320.0786-0.7073-0.26610.10561.00411.5336-0.3044-0.49771.10810.1543-0.12910.73030.05650.5206-79.9696-4.827833.4645
265.47510.8680.32044.3378-1.35393.78860.3247-0.1629-0.90780.07020.1565-0.66530.76020.0211-0.44490.9779-0.0533-0.12210.7465-0.08350.5202-84.2796-3.15251.2796
277.7539-5.521-4.17734.36551.77425.5719-0.33590.4018-0.0786-0.393-0.3273-0.2304-0.06660.71650.59830.8501-0.0105-0.0560.9148-0.11120.6897-87.8263-2.956210.7461
289.55169.6604-3.76332.0048-0.75827.747-0.4363-0.47730.34180.1159-0.4118-0.7476-0.6908-0.48360.67621.03160.0443-0.26980.79970.04220.6652-76.4193-4.025323.9958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain "A" and resseq 343:382A343 - 382
2X-RAY DIFFRACTION2chain "A" and resseq 383:429A383 - 429
3X-RAY DIFFRACTION3chain "A" and resseq 18:30A18 - 30
4X-RAY DIFFRACTION4chain "A" and resseq 3:17A3 - 17
5X-RAY DIFFRACTION5chain "A" and resseq 31:154A31 - 154
6X-RAY DIFFRACTION6chain "A" and resseq 430:455A430 - 455
7X-RAY DIFFRACTION7chain "A" and resseq 239:322A239 - 322
8X-RAY DIFFRACTION8chain "A" and resseq 456:482A456 - 482
9X-RAY DIFFRACTION9chain "A" and not ( resseq 343:382 or resseq 383:429 or resseq 31:154 or resseq 430:455 or resseq 239:322 or resseq 2:17 or resseq 18:30 or resseq 456:482 )A155 - 238
10X-RAY DIFFRACTION9chain "A" and not ( resseq 343:382 or resseq 383:429 or resseq 31:154 or resseq 430:455 or resseq 239:322 or resseq 2:17 or resseq 18:30 or resseq 456:482 )A323 - 342
11X-RAY DIFFRACTION9chain "A" and not ( resseq 343:382 or resseq 383:429 or resseq 31:154 or resseq 430:455 or resseq 239:322 or resseq 2:17 or resseq 18:30 or resseq 456:482 )A483 - 700
12X-RAY DIFFRACTION10chain "B" and resseq 343:382B343 - 382
13X-RAY DIFFRACTION11chain "B" and resseq 383:429B383 - 429
14X-RAY DIFFRACTION12chain "B" and resseq 18:30B18 - 30
15X-RAY DIFFRACTION13chain "B" and resseq 3:17B3 - 17
16X-RAY DIFFRACTION14chain "B" and resseq 31:154B31 - 154
17X-RAY DIFFRACTION15chain "B" and resseq 430:455B430 - 455
18X-RAY DIFFRACTION16chain "B" and resseq 239:322B239 - 322
19X-RAY DIFFRACTION17chain "B" and resseq 456:482B456 - 482
20X-RAY DIFFRACTION18chain "B" and not ( resseq 343:382 or resseq 383:429 or resseq 31:154 or resseq 430:455 or resseq 239:322 or resseq 2:17 or resseq 18:30 or resseq 456:482 )B155 - 238
21X-RAY DIFFRACTION18chain "B" and not ( resseq 343:382 or resseq 383:429 or resseq 31:154 or resseq 430:455 or resseq 239:322 or resseq 2:17 or resseq 18:30 or resseq 456:482 )B323 - 342
22X-RAY DIFFRACTION18chain "B" and not ( resseq 343:382 or resseq 383:429 or resseq 31:154 or resseq 430:455 or resseq 239:322 or resseq 2:17 or resseq 18:30 or resseq 456:482 )B483 - 700
23X-RAY DIFFRACTION19chain "C" and resseq 539:581C539 - 581
24X-RAY DIFFRACTION20chain "C" and resseq 610:634C610 - 634
25X-RAY DIFFRACTION21chain "C" and not ( resseq 539:581 or resseq 610:634 )C415 - 538
26X-RAY DIFFRACTION21chain "C" and not ( resseq 539:581 or resseq 610:634 )C582 - 609
27X-RAY DIFFRACTION21chain "C" and not ( resseq 539:581 or resseq 610:634 )C635 - 742
28X-RAY DIFFRACTION22chain "D" and resseq 539:581D539 - 581
29X-RAY DIFFRACTION23chain "D" and resseq 610:634D610 - 634
30X-RAY DIFFRACTION24chain "D" and not ( resseq 539:581 or resseq 610:634 )D415 - 538
31X-RAY DIFFRACTION24chain "D" and not ( resseq 539:581 or resseq 610:634 )D582 - 609
32X-RAY DIFFRACTION24chain "D" and not ( resseq 539:581 or resseq 610:634 )D635 - 742
33X-RAY DIFFRACTION25( chain "E" or chain "F" ) and not ( resid 0 or resid 100 )E9 - 15
34X-RAY DIFFRACTION25( chain "E" or chain "F" ) and not ( resid 0 or resid 100 )H - B0 - 502
35X-RAY DIFFRACTION26( chain "G" or chain "H" ) and not ( resid 0 or resid 100 )G9 - 15
36X-RAY DIFFRACTION26( chain "G" or chain "H" ) and not ( resid 0 or resid 100 )F - A0 - 502
37X-RAY DIFFRACTION27( chain "E" or chain "F" ) and ( resid 0 or resid 100 )E9 - 15
38X-RAY DIFFRACTION27( chain "E" or chain "F" ) and ( resid 0 or resid 100 )H - B0 - 502
39X-RAY DIFFRACTION28( chain "G" or chain "H" ) and ( resid 0 or resid 100 )G9 - 15
40X-RAY DIFFRACTION28( chain "G" or chain "H" ) and ( resid 0 or resid 100 )F - A0 - 502

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