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- PDB-4z53: Quinolone(Trovafloxacin)-DNA cleavage complex of topoisomerase IV... -

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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) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding
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 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 gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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)

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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-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

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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)

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