[English] 日本語
Yorodumi
- PDB-4z53: Quinolone(Trovafloxacin)-DNA cleavage complex of topoisomerase IV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z53
TitleQuinolone(Trovafloxacin)-DNA cleavage complex of topoisomerase IV from S. pneumoniae
Components
  • (E-site DNA) x 4
  • DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A
KeywordsISOMERASE / Topo IV / Cleavage complex / DNA / quinolone
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 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / 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 ...DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / 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 / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / 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 serotype 4 (bacteria)
Streptococcus pneumoniae TIGR4 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsLaponogov, I. / Veselkov, D.A. / Pan, X.-S. / Selvarajah, J. / Crevel, I.M.-T. / Fisher, L.M. / Sanderson, M.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K010069/1 United Kingdom
CitationJournal: To Be Published
Title: Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae
Authors: Laponogov, I. / Veselkov, D.A. / Pan, X.-S. / Selvarajah, J. / Crevel, I.M.-T. / Fisher, L.M. / Sanderson, M.R.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A
B: DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A
E: E-site DNA
F: E-site DNA
G: E-site DNA
H: E-site DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,29412
Polymers179,3646
Non-polymers9306
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15270 Å2
ΔGint-105 kcal/mol
Surface area57340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.830, 157.830, 210.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 84211.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria), (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: parE, SP_0852, parC, SP_0855 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59961, UniProt: P72525, EC: 5.99.1.3

-
DNA chain , 4 types, 4 molecules EFGH

#2: DNA chain E-site DNA


Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain E-site DNA


Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain E-site DNA


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain E-site DNA


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

-
Non-polymers , 3 types, 10 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.82 Å3/Da / Density % sol: 74.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM Na cacodylate, 100-150 mM NaCl, 4-7% isopropanol
PH range: 6.0-7.0 / Temp details: incubator

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.01→73.9 Å / Num. obs: 60603 / % possible obs: 99.95 % / Redundancy: 10.07 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.9094
Reflection shellResolution: 3.01→3.09 Å / Redundancy: 10.38 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 0.75 / % possible all: 99.92

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K9F
Resolution: 3.26→73.896 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 2403 5.02 %Random
Rwork0.1732 ---
obs0.175 47829 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.26→73.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10286 730 64 4 11084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311352
X-RAY DIFFRACTIONf_angle_d0.70915599
X-RAY DIFFRACTIONf_dihedral_angle_d15.4364103
X-RAY DIFFRACTIONf_chiral_restr0.0461797
X-RAY DIFFRACTIONf_plane_restr0.0021912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2601-3.32670.27371560.21492603X-RAY DIFFRACTION100
3.3267-3.3990.24041400.20552617X-RAY DIFFRACTION100
3.399-3.47810.2661670.19522619X-RAY DIFFRACTION100
3.4781-3.5650.22941330.18812654X-RAY DIFFRACTION100
3.565-3.66140.2261220.18652678X-RAY DIFFRACTION100
3.6614-3.76920.22511470.17812627X-RAY DIFFRACTION100
3.7692-3.89080.221170.17092648X-RAY DIFFRACTION100
3.8908-4.02990.23431030.16282706X-RAY DIFFRACTION100
4.0299-4.19120.17861570.1552612X-RAY DIFFRACTION100
4.1912-4.38190.17191350.14282705X-RAY DIFFRACTION100
4.3819-4.61290.16231520.13542637X-RAY DIFFRACTION100
4.6129-4.90190.20311550.14592657X-RAY DIFFRACTION100
4.9019-5.28030.18521150.16172722X-RAY DIFFRACTION100
5.2803-5.81140.2161630.18772651X-RAY DIFFRACTION100
5.8114-6.65190.25161520.19782701X-RAY DIFFRACTION100
6.6519-8.37880.19331340.18172748X-RAY DIFFRACTION100
8.3788-73.91540.19131550.18422841X-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)
10.62480.5778-0.06418.5679-6.16425.2051-0.0681-0.1504-0.07520.374-0.0295-0.66690.14020.2270.08620.51910.03110.01040.4905-0.07280.3438-0.5274176.1409255.1031
22.11711.70130.28876.89920.07368.53030.1853-0.38060.09250.2859-0.2126-0.6074-0.34690.28620.03160.37410.02050.04120.45840.02170.46696.5022198.6079237.9109
39.69321.1892-5.09833.6537-3.00854.32230.57081.2383-0.35450.58960.46170.5368-0.7641-0.1716-0.83140.84850.3947-0.1530.939-0.26750.532510.1411143.4934249.9991
40.2798-0.88350.53784.0222-2.4331.4295-0.24290.74660.18440.2716-0.3184-1.49940.1821.78220.53480.53730.3365-0.47811.5936-0.48381.231526.7584134.754246.2732
52.81741.49471.1043.291.07383.7283-0.15490.1438-0.3241-0.30340.25610.090.09060.1975-0.09660.69180.03990.00770.38910.01610.3701-5.8104152.455241.8576
64.5963-2.72611.58993.8277-4.85647.6957-0.12240.7828-0.43860.95620.21750.4387-1.2119-0.21850.13550.818-0.0345-0.09040.6013-0.14310.4218-6.1891188.307254.9732
74.62431.17960.61044.11262.47253.2296-0.15330.0887-0.09750.01160.20920.68050.5516-0.6489-0.05360.9063-0.21070.02550.6020.14930.6431-26.0678124.2156254.1985
84.89332.48750.73847.99322.53542.0085-0.0439-0.01090.4126-0.0468-0.05530.3835-0.2977-0.20370.0970.59540.13830.02460.38340.01270.2321-14.8166159.7195263.0773
92.25170.82320.30233.1204-0.26212.37120.1729-0.113-0.36180.50850.0666-0.05950.72270.2366-0.21450.85820.162-0.060.4261-0.0170.4392-7.5056146.132264.1769
10-0.03840.07930.44068.21753.88453.4902-0.07240.07750.1176-0.03220.01860.41860.2657-0.26380.10880.33620.00940.06650.51780.07250.3891-1.7877178.6471204.9464
113.99011.311.5476.6409-1.55397.84210.33670.50550.12510.2855-0.04270.5165-0.4811-0.39-0.3050.42170.14150.04360.5532-0.01320.3387-4.4831200.6487224.3594
123.07270.755-4.42891.8283-0.40866.6533-0.3329-1.6497-0.32040.52410.5863-0.2989-0.4516-0.7777-0.19610.61320.035-0.17241.06530.2860.5771-15.5366146.2224207.1067
132.82951.5126-1.963.1752-0.44021.52460.009-0.48280.7322-0.32940.47530.2366-0.4949-1.1115-0.430.44080.05660.00451.26650.33321.1911-32.3805138.9983209.9566
142.5659-1.18330.53315.3436-1.25824.0678-0.1619-0.0858-0.11460.57560.25060.134-0.4838-0.0894-0.07150.55470.07140.06230.39530.00130.35661.02153.4347216.0668
154.68463.06271.52384.22824.64916.7499-0.27510.0513-0.0341-0.7730.8993-0.2181-1.00510.2776-0.46150.81260.0429-0.01360.61080.07970.4355.2804189.6195206.1119
167.1113-1.2029-0.2913.8597-1.18234.0630.1292-0.1397-0.02610.19210.0615-0.33340.18430.4867-0.18630.64190.03440.03420.436-0.14070.55520.1903125.6204201.187
172.9514-1.42661.48653.6887-1.67492.883-0.42490.3186-0.03280.289-0.0439-0.4949-0.25320.17270.4930.5896-0.06510.08590.57530.0240.352110.566161.5306195.6823
182.0659-0.3958-0.23462.80960.79081.84870.03290.3192-0.0363-0.46120.2618-0.06620.1027-0.1381-0.30590.6934-0.01840.03040.48690.02320.35472.3187149.085193.3608
191.71181.7469-1.52438.196-3.36753.0104-0.3865-0.3981.66510.06420.82010.8339-0.38420.9306-0.3180.65330.1471-0.14851.0952-0.30051.013825.0237151.6361233.3118
202.26631.65141.75183.1232-0.61873.3744-0.5592-1.3853-0.27670.42810.7148-0.2548-0.0551-0.0942-0.20751.08150.4944-0.31451.3404-0.03891.030918.7901130.425257.2486
211.49620.3647-0.76810.8460.17282.0951-0.47510.2097-0.36830.14840.4228-0.63970.38670.58750.08540.89550.4418-0.04881.1267-0.23620.941121.1112128.734234.7529
221.8836-2.8291-0.28024.79131.49332.0905-0.2105-2.37531.36240.47140.82630.9508-0.1258-0.4407-0.47790.48750.06690.15371.2405-0.06941.2633-29.7383154.1438224.8975
232.0028-0.8719-0.40573.85961.27935.9870.22650.6428-0.0182-1.05010.27360.6797-0.654-0.5216-0.44831.0652-0.3396-0.28780.98650.14780.9922-25.0889134.7527198.5955
242.5917-0.7454-0.96832.434-1.01331.4361-0.2947-0.481-0.81210.29770.43870.95860.3412-0.4238-0.08780.7208-0.2550.03821.01760.38761.1324-27.3015130.9708220.7569
250.53310.4741-1.09860.4658-0.93162.71780.34620.43340.19990.35270.64140.5794-0.0076-1.2329-0.93661.23660.11110.13621.28570.36761.5055-25.4749154.8811205.7149
265.8194-1.8136-0.00995.10071.90812.55950.32620.4477-0.9102-0.40930.1380.73791.03910.0039-0.50851.29290.2324-0.20180.9590.03110.7078-0.9973131.7382244.0733
276.22970.56630.58864.6536-2.24033.24240.2576-0.3868-1.04090.23350.2444-0.43090.70580.2667-0.52991.0928-0.0234-0.15510.9825-0.080.6632-5.2949133.3778211.8464
283.9877-3.2253-3.76743.65481.03847.4041-0.2874-0.41530.1065-0.0014-0.42640.4985-0.6870.13040.5361.25490.2866-0.33471.3142-0.43031.1605-8.9375133.5497221.3987
299.77024.7972-3.65564.94040.15272.8319-0.4436-0.32830.02090.3139-0.5639-0.8949-0.7499-0.30690.88511.2209-0.1787-0.21351.19830.07820.90032.5739132.4972234.5497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain "A" and resseq 1343:1382
2X-RAY DIFFRACTION2chain "A" and resseq 1383:1429
3X-RAY DIFFRACTION3chain "A" and resseq 1018:1030
4X-RAY DIFFRACTION4chain "A" and resseq 1002:1017
5X-RAY DIFFRACTION5chain "A" and resseq 1031:1154
6X-RAY DIFFRACTION6chain "A" and resseq 1430:1455
7X-RAY DIFFRACTION7chain "A" and resseq 1239:1322
8X-RAY DIFFRACTION8chain "A" and resseq 1456:1484
9X-RAY DIFFRACTION9chain "A" and (resseq 1155:1238 or resseq 1323:1342)
10X-RAY DIFFRACTION10chain "B" and resseq 1343:1382
11X-RAY DIFFRACTION11chain "B" and resseq 1383:1429
12X-RAY DIFFRACTION12chain "B" and resseq 1018:1030
13X-RAY DIFFRACTION13chain "B" and resseq 1002:1017
14X-RAY DIFFRACTION14chain "B" and resseq 1031:1154
15X-RAY DIFFRACTION15chain "B" and resseq 1430:1455
16X-RAY DIFFRACTION16chain "B" and resseq 1239:1322
17X-RAY DIFFRACTION17chain "B" and resseq 1456:1484
18X-RAY DIFFRACTION18chain "B" and (resseq 1155:1238 or resseq 1323:1342)
19X-RAY DIFFRACTION19chain "A" and resseq 539:581
20X-RAY DIFFRACTION20chain "A" and resseq 610:634
21X-RAY DIFFRACTION21chain "A" and (resseq 415:538 or resseq 582:609 or resseq 635:640 or resid 742)
22X-RAY DIFFRACTION22chain "B" and resseq 539:581
23X-RAY DIFFRACTION23chain "B" and resseq 610:634
24X-RAY DIFFRACTION24chain "B" and (resseq 415:538 or resseq 582:609 or resseq 635:640 or resid 742)
25X-RAY DIFFRACTION25chain "B" and resseq 641:643
26X-RAY DIFFRACTION26(chain "E" or chain "F" ) and resid 1:15
27X-RAY DIFFRACTION27(chain "G" or chain "H" ) and resid 1:15
28X-RAY DIFFRACTION28(chain "E" or chain "F" ) and (resid 0 or resid 100)
29X-RAY DIFFRACTION29(chain "G" or chain "H" ) and (resid 0 or resid 100)

+
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://pdbjlvh1.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