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- PDB-4kpe: Novel fluoroquinolones in complex with topoisomerase IV from S. p... -

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Basic information

Entry
Database: PDB / ID: 4kpe
TitleNovel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate
Components
  • (DNA topoisomerase 4 subunit ...Topoisomerase) 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 / ACHN-245
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
Chem-AF5 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsLaponogov, I. / Pan, X.-S. / Vesekov, D.A. / Cirz, R.T. / Wagman, A.S. / Moser, H.E. / Fisher, L.M. / Sanderson, M.R.
CitationJournal: Open Biol / Year: 2016
Title: Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones.
Authors: Laponogov, I. / Pan, X.S. / Veselkov, D.A. / Cirz, R.T. / Wagman, A. / Moser, H.E. / Fisher, L.M. / Sanderson, M.R.
History
DepositionMay 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / pdbx_entity_src_syn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Jan 29, 2020Group: Data collection / Database references / Derived calculations
Category: reflns / struct_conn / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)185,56816
Polymers184,6848
Non-polymers8858
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.830, 157.830, 210.710
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 / 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 / Topoisomerase


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 / Source: (synth.) synthetic construct (others)
#4: DNA chain E-site DNA2


Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain E-site DNA3


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain E-site DNA4


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 32 molecules

#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-AF5 / (7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid


Mass: 369.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20FN3O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.1 Å3/Da / Density % sol: 70.02 %
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: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2011
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.43→41.819 Å / Num. all: 41232 / Num. obs: 40043 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.16 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.38
Reflection shellResolution: 3.43→3.52 Å / Redundancy: 5.22 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 6.37 / % possible all: 98.2

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Processing

Software
NameVersionClassification
GDEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.43→41.819 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 2003 5.01 %Random
Rwork0.1541 ---
obs0.1562 40016 97.13 %-
all-40043 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.43→41.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10388 730 60 24 11202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911462
X-RAY DIFFRACTIONf_angle_d1.2415726
X-RAY DIFFRACTIONf_dihedral_angle_d18.5674216
X-RAY DIFFRACTIONf_chiral_restr0.0771810
X-RAY DIFFRACTIONf_plane_restr0.0041922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.43-3.51570.23861340.18252722X-RAY DIFFRACTION98
3.5157-3.61070.19051440.17952688X-RAY DIFFRACTION99
3.6107-3.71690.22671400.16762719X-RAY DIFFRACTION98
3.7169-3.83680.22491450.15572721X-RAY DIFFRACTION98
3.8368-3.97390.16721480.14562688X-RAY DIFFRACTION98
3.9739-4.13280.17961340.13882723X-RAY DIFFRACTION98
4.1328-4.32070.16771470.13142719X-RAY DIFFRACTION98
4.3207-4.54830.15421440.12742710X-RAY DIFFRACTION97
4.5483-4.83290.19871400.13422698X-RAY DIFFRACTION98
4.8329-5.20540.21071470.14792723X-RAY DIFFRACTION97
5.2054-5.7280.20761450.16022728X-RAY DIFFRACTION97
5.728-6.55410.22021440.17312724X-RAY DIFFRACTION97
6.5541-8.24710.17961480.15562740X-RAY DIFFRACTION96
8.2471-41.82170.19421430.16972710X-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)
1-0.19930.75850.42533.0454.01872.7454-0.0741-0.02030.10850.4315-0.06690.54090.1342-0.14740.12190.4372-0.0360.01020.34730.04840.250579.475-39.523744.45
23.72260.8317-0.27164.6875-0.15185.31390.057-0.2696-0.05910.0075-0.17940.66440.1283-0.48230.11720.21820.019-0.030.2996-0.0350.298172.4329-61.952327.2819
34.1298-1.54173.88061.6186-2.69615.11610.39371.08590.66540.34050.2003-0.15980.5328-0.2615-0.40450.50710.24250.0450.48630.07460.41868.5561-7.089339.2846
41.1191-0.5001-0.64151.21870.30421.8108-0.1997-0.32960.1411-0.5873-0.20140.36650.068-1.50540.56490.47090.22320.2340.90190.08990.817751.49541.466935.2552
51.44040.2151-0.51532.075-1.10192.86880.00650.1436-0.0048-0.23360.0297-0.0268-0.05670.0402-0.04920.46570.0159-0.02470.2187-0.03510.215684.8462-15.732530.9988
62.6277-2.8756-1.33268.34794.58145.8952-0.0050.49790.15130.56210.0811-0.42580.5657-0.04270.12880.4599-0.05660.0450.42810.07220.203885.1179-51.677444.3646
73.02940.76280.1995.5937-0.95293.3161-0.04210.1325-0.0131-0.07810.1427-0.761-0.44840.6034-0.19630.4984-0.1186-0.00590.3383-0.09760.3779104.820512.477843.5237
81.330.9005-0.62432.8228-1.00412.37580.02650.1847-0.31540.1759-0.0534-0.44170.17230.14090.10520.45880.0952-0.06760.22790.03560.168393.2654-24.467951.9409
90.84720.0513-0.16951.39640.04670.9770.0295-0.17110.10320.32950.0226-0.0354-0.2237-0.0383-0.04130.60320.0515-0.00840.312-0.02670.224986.5114-9.431553.3322
10-0.02610.36680.07585.8753-3.45312.5745-0.0987-0.01640.0412-0.045-0.0689-0.4-0.14030.21360.16060.27430.0492-0.03020.3604-0.08740.230380.6595-41.9395-5.6284
113.09080.8125-1.28724.6690.1564.47060.1175-0.09720.22550.33080.1439-0.29720.31320.2596-0.13230.23960.0665-0.06520.3334-0.01010.218583.3838-63.955813.739
127.2072-2.70035.5752.5893-1.06235.96060.1328-1.31340.0408-0.06820.630.32830.82430.1008-0.35940.4882-0.0630.10430.5382-0.19770.312994.3648-9.7446-3.3022
132.3696-0.78051.10970.350.54798.24280.22670.11590.2670.152-0.0559-0.82550.42541.5388-0.30280.48990.01570.07870.6362-0.09970.7994111.904-2.47130.1021
141.12780.0089-0.19162.51991.11052.8137-0.0539-0.04840.02640.23060.11740.00620.0868-0.03-0.04010.44970.051-0.03660.25470.00220.20177.7992-16.70085.6912
153.74661.8435-0.28036.7819-2.5863.7407-0.1742-0.26250.0113-0.7020.71250.42630.8059-0.409-0.28650.40860.0758-0.04570.3352-0.02320.231773.6115-52.9121-4.5006
162.9640.09790.26344.1253-0.95813.01970.0275-0.10220.12590.21670.19060.334-0.2484-0.371-0.20980.4170.0573-0.07370.28230.09810.390658.857211.0802-9.2108
171.7641-2.2387-0.33173.97320.77960.8439-0.3540.3429-0.2808-0.0681-0.23330.99020.0288-0.34330.27420.5357-0.0871-0.10180.36080.02060.149368.5949-26.2951-14.1018
181.1263-0.32340.76850.6963-0.06371.05680.05670.2850.1739-0.31530.04770.0676-0.05380.0004-0.16660.59460.0059-0.04690.35960.04180.237676.3664-12.3325-17.0101
190.93810.45341.6583.1464.81668.39120.0259-0.9948-1.38790.71370.3583-0.17361.1514-0.7789-0.29220.69290.03130.07520.69040.29711.120153.5553-14.975122.8773
201.9679-0.0098-1.2643.03761.16162.7408-0.0225-0.0470.40310.222-0.08360.0409-0.7884-0.58660.11360.79630.36910.09580.8684-0.07730.509359.82325.719246.4792
210.5265-0.0760.37740.5883-0.05412.7132-0.1338-0.00190.1612-0.12980.10530.3192-0.4434-0.59850.03920.63590.3076-0.00910.69030.06170.541457.67877.543424.0238
223.13660.38742.15239.4293-7.96128.6948-0.41770.1821-0.9619-0.82490.6036-0.09221.52611.1369-0.18710.84410.2175-0.05710.6635-0.20591.043109.2718-17.51814.1452
233.86350.3817-0.03156.0556-1.71842.8786-0.32480.9463-0.1023-0.74820.4063-0.8882-0.14650.41710.11680.7354-0.27730.17580.7613-0.07360.5841104.44871.8901-11.5246
241.150.54340.86041.07950.91962.5628-0.0972-0.02670.14550.05420.1223-0.4396-0.44970.47390.03050.5639-0.21360.00880.647-0.12040.6004106.30915.584810.4889
252.5966-1.1893-1.92371.7711-1.26754.00460.3209-0.21940.5498-0.27460.0084-0.182-0.9280.3526-0.38570.88860.05680.0050.4892-0.12530.459880.04854.60531.9366
262.6980.8296-2.39250.96550.83853.53680.42910.28010.444-0.03750.07230.0062-0.9559-0.1216-0.47230.86080.01680.0060.56670.09950.425783.81453.17582.8967
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 3:17A2 - 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 - 852
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 3:17B2 - 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 - 840
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 - 830
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 - 832
33X-RAY DIFFRACTION25chain "E" or chain "F"E9 - 15
34X-RAY DIFFRACTION26chain "G" or chain "H"G9 - 15

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Yorodumi

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  • 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

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