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- PDB-4bul: Novel hydroxyl tricyclics (e.g. GSK966587) as potent inhibitors o... -

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Basic information

Entry
Database: PDB / ID: 4bul
TitleNovel hydroxyl tricyclics (e.g. GSK966587) as potent inhibitors of bacterial type IIA topoisomerases
Components
  • 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP *CP*GP*CP*AP*C)-3'
  • 5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*TP*AP*CP*CP*TP *AP*CP*GP*GP*CP*T)-3'
  • DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
KeywordsISOMERASE / TYPE IIA TOPOISOMERASES / NBTIS
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / 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 gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...Rossmann fold - #670 / DNA gyrase, subunit A / 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 gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. / 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 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-AE8 / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMiles, T.J. / Hennessy, A.J. / Bax, B. / Brooks, G. / Brown, B.S. / Brown, P. / Cailleau, N. / Chen, D. / Dabbs, S. / Davies, D.T. ...Miles, T.J. / Hennessy, A.J. / Bax, B. / Brooks, G. / Brown, B.S. / Brown, P. / Cailleau, N. / Chen, D. / Dabbs, S. / Davies, D.T. / Esken, J.M. / Giordano, I. / Hoover, J.L. / Huang, J. / Jones, G.E. / Sukmar, S.K.K. / Spitzfaden, C. / Markwell, R.E. / Minthorn, E.A. / Rittenhouse, S. / Gwynn, M.N. / Pearson, N.D.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Novel Hydroxyl Tricyclics (E.G., Gsk966587) as Potent Inhibitors of Bacterial Type Iia Topoisomerases.
Authors: Miles, T.J. / Hennessy, A.J. / Bax, B. / Brooks, G. / Brown, B.S. / Brown, P. / Cailleau, N. / Chen, D. / Dabbs, S. / Davies, D.T. / Esken, J.M. / Giordano, I. / Hoover, J.L. / Huang, J. / ...Authors: Miles, T.J. / Hennessy, A.J. / Bax, B. / Brooks, G. / Brown, B.S. / Brown, P. / Cailleau, N. / Chen, D. / Dabbs, S. / Davies, D.T. / Esken, J.M. / Giordano, I. / Hoover, J.L. / Huang, J. / Jones, G.E. / Kusalakumari Sukmar, S.K. / Spitzfaden, C. / Markwell, R.E. / Minthorn, E.A. / Rittenhouse, S. / Gwynn, M.N. / Pearson, N.D.
#1: Journal: Nature / Year: 2010
Title: Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents.
Authors: Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / ...Authors: Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / Lewis, C.J. / May, E.W. / Saunders, M.R. / Singh, O. / Spitzfaden, C.E. / Shen, C. / Shillings, A. / Theobald, A.J. / Wohlkonig, A. / Pearson, N.D. / Gwynn, M.N.
History
DepositionJun 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 18, 2013Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_alt_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_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_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
C: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
E: 5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*TP*AP*CP*CP*TP *AP*CP*GP*GP*CP*T)-3'
F: 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP *CP*GP*CP*AP*C)-3'
G: 5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*TP*AP*CP*CP*TP *AP*CP*GP*GP*CP*T)-3'
H: 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP *CP*GP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,44511
Polymers180,7586
Non-polymers6875
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16050 Å2
ΔGint-77.8 kcal/mol
Surface area57420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.871, 93.871, 416.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A


Mass: 78109.000 Da / Num. of mol.: 2
Fragment: GYRA N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491, GYRB C-TERMINAL 27KDA DOMAIN, RESIDUES 410-644
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FUSION TRUNCATE WITH DELETION AND Y123F GYRB27A56GKDELY123F (BAX ET AL., 2010)
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P66937, UniProt: Q99XG5, EC: 5.99.1.3, EC: 5.99.1.3

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DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain 5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*TP*AP*CP*CP*TP *AP*CP*GP*GP*CP*T)-3'


Mass: 6156.963 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP *CP*GP*CP*AP*C)-3'


Mass: 6112.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 453 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-AE8 / (S)-4-((4-(((2,3-dihydro-[1,4]dioxino[2,3-c]pyridin-7-yl)methyl)amino)piperidin-1-yl)methyl)-3-fluoro-4-hydroxy-4H-pyrrolo[3,2,1-de][1,5]naphthyridin-7(5H)-one


Mass: 467.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26FN5O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsGSK966587 (S)-4-((4-(((2,3-DIHYDRO-[1,4]DIOXINO[2, 3-C]PYRIDIN-7-YL)METHYL)AMINO)PIPERIDIN-1-YL) ...GSK966587 (S)-4-((4-(((2,3-DIHYDRO-[1,4]DIOXINO[2, 3-C]PYRIDIN-7-YL)METHYL)AMINO)PIPERIDIN-1-YL)METHYL)- 3-FLUORO-4-HYDROXY-4H-PYRROLO[3,2,1-DE][1,5] NAPHTHYRIDIN-7(5H)-ONE
Sequence detailsC-TERMINAL DOMAIN (410-644) WITH GREEK KEY DOMAIN (544-579) DELETED AND REPLACED WITH TWO RESIDUES, ...C-TERMINAL DOMAIN (410-644) WITH GREEK KEY DOMAIN (544-579) DELETED AND REPLACED WITH TWO RESIDUES, TG. CATALYTIC TYROSINE MUTATED TO PHENYLALANINE, Y123F.

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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: 3.15 Å3/Da / Density % sol: 60.94 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96865
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96865 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.803
11K, H, -L20.197
ReflectionResolution: 2.6→81.38 Å / Num. obs: 60721 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XCS

2xcs


Resolution: 2.6→24.79 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.49 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.18277 1844 3 %RANDOM
Rwork0.14376 ---
obs0.14494 58754 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.6→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10637 1587 38 448 12710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01812709
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.85617491
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09551355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68723.678541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74152025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.61215120
X-RAY DIFFRACTIONr_chiral_restr0.0740.21882
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219169
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8742.4235411
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4183.6326769
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0912.4547298
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.19920.89919006
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 122 -
Rwork0.204 4357 -
obs--96.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0074-0.1452-0.51961.70210.25611.61120.0282-0.24980.15460.14830.00450.0198-0.0917-0.0948-0.03270.2146-0.04380.0280.1807-0.02980.012313.941254.505863.7872
21.1922-0.3287-0.0471.2455-0.07271.1370.00170.0761-0.1989-0.00310.0064-0.02050.09620.0277-0.00820.1137-0.03880.01410.1027-0.0370.04429.992428.800634.4669
36.18713.50680.08022.06210.30851.15510.01210.301-0.1535-0.05960.1564-0.1252-0.28930.2321-0.16850.284-0.00480.03090.2655-0.04310.254229.0958-1.531541.4149
46.77360.60680.53711.4465-0.09780.079-0.1646-0.003-0.28080.09120.1344-0.12590.0551-0.02420.03020.3443-0.02640.07960.21580.0020.240811.8262-13.597646.0532
54.0149-1.4476-0.34282.12931.30655.0106-0.0184-0.56250.01990.5328-0.0886-0.2190.0930.4780.1070.293-0.1061-0.06690.29210.03630.09733.10746.959661.785
62.8855-0.1344-0.44121.457-0.18392.00090.08990.31990.3072-0.099-0.0165-0.0236-0.3354-0.005-0.07340.2459-0.00340.03580.25930.03110.0490.166253.905616.3603
71.08910.2464-0.19821.10490.08921.1533-0.0111-0.0296-0.17880.0047-0.01780.05370.063-0.00090.02890.1256-0.0180.02240.09360.00140.0416-19.540833.288247.3127
86.4128-2.5494-1.87346.88282.28882.0932-0.12630.12420.2069-0.05950.09130.1781-0.0248-0.11270.0350.2455-0.08180.01210.1098-0.00440.1499-22.44572.886343.3208
95.4202-0.8062-0.61862.173-0.66720.8882-0.05170.001-0.2498-0.1815-0.0508-0.07130.09720.12080.10250.225-0.07930.03430.14770.01150.1604-7.0446-12.161540.8522
103.21650.3575-0.67961.3662-0.92875.71030.10150.579-0.0079-0.3957-0.10330.2926-0.0307-0.40970.00180.25470.0454-0.02960.3199-0.0140.1502-20.225350.117619.0598
112.965-0.25011.74890.6087-0.28551.0767-0.42840.11440.54590.05140.1255-0.0312-0.30850.02960.30290.24790.00340.01020.2385-0.00240.15115.936351.52140.2998
125.6132-0.68352.04820.3197-0.26030.7623-0.35190.01120.8708-0.03120.0517-0.1322-0.1840.00190.30030.2781-0.03730.04480.2098-0.01610.17445.929351.546840.3279
131.678-0.057-0.57892.1033-0.85762.63970.04840.12620.28230.0690.00720.0943-0.6616-0.0691-0.05560.2966-0.01990.03490.1746-0.03260.087930.896355.433513.7007
142.09090.1169-0.30362.62231.09151.77510.02-0.06770.2992-0.05750.019-0.0938-0.48630.0925-0.0390.3055-0.02090.02670.17290.04360.0758-16.738261.325366.2746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A417 - 608
2X-RAY DIFFRACTION2A1029 - 1244
3X-RAY DIFFRACTION2A1328 - 1369
4X-RAY DIFFRACTION2A1461 - 1491
5X-RAY DIFFRACTION3A1370 - 1379
6X-RAY DIFFRACTION3A1451 - 1460
7X-RAY DIFFRACTION4A1380 - 1450
8X-RAY DIFFRACTION5A1008 - 1028
9X-RAY DIFFRACTION5A609 - 640
10X-RAY DIFFRACTION6C416 - 608
11X-RAY DIFFRACTION7C1029 - 1244
12X-RAY DIFFRACTION7C1328 - 1369
13X-RAY DIFFRACTION7C1461 - 1490
14X-RAY DIFFRACTION8C1370 - 1379
15X-RAY DIFFRACTION8C1451 - 1460
16X-RAY DIFFRACTION9C1380 - 1450
17X-RAY DIFFRACTION10C1010 - 1028
18X-RAY DIFFRACTION10C609 - 639
19X-RAY DIFFRACTION11E2 - 20
20X-RAY DIFFRACTION11F2 - 19
21X-RAY DIFFRACTION12G2 - 19
22X-RAY DIFFRACTION12H2 - 20
23X-RAY DIFFRACTION13A1245 - 1327
24X-RAY DIFFRACTION14C1245 - 1327

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  • 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

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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

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