[English] 日本語
Yorodumi
- PDB-6qx1: 2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qx1
Title2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA.
Components
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
KeywordsISOMERASE / Inhibitor / DNA complex
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) 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
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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A ...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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / 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
Similarity search - Domain/homology
GLYCINE / Chem-JK8 / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsBax, B.D.
Funding support1items
OrganizationGrant numberCountry
European Union115583
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.
Authors: Thalji, R.K. / Raha, K. / Andreotti, D. / Checchia, A. / Cui, H. / Meneghelli, G. / Profeta, R. / Tonelli, F. / Tommasi, S. / Bakshi, T. / Donovan, B.T. / Howells, A. / Jain, S. / Nixon, C. ...Authors: Thalji, R.K. / Raha, K. / Andreotti, D. / Checchia, A. / Cui, H. / Meneghelli, G. / Profeta, R. / Tonelli, F. / Tommasi, S. / Bakshi, T. / Donovan, B.T. / Howells, A. / Jain, S. / Nixon, C. / Quinque, G. / McCloskey, L. / Bax, B.D. / Neu, M. / Chan, P.F. / Stavenger, R.A.
History
DepositionMar 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 24, 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_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: DNA gyrase subunit B
A: DNA gyrase subunit A
D: DNA gyrase subunit B
C: DNA gyrase subunit A
E: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
F: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,96617
Polymers168,5566
Non-polymers1,41111
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22310 Å2
ΔGint-122 kcal/mol
Surface area56870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.190, 93.190, 408.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12A
22C
13E
23F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTYRTYRBA417 - 6399 - 197
21LYSLYSTYRTYRDC417 - 6399 - 197
12ASNASNGLNGLNAB10 - 4899 - 488
22ASNASNGLNGLNCD10 - 4899 - 488
13DADADTDTEE1 - 20201 - 20
23DADADTDTFF1 - 20201 - 20

NCS ensembles :
ID
1
2
3

-
Components

-
DNA gyrase subunit ... , 2 types, 4 molecules BDAC

#1: Protein DNA gyrase subunit B /


Mass: 22605.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli)
References: UniProt: P66937, UniProt: P0A0K8*PLUS, EC: 5.99.1.3
#2: Protein DNA gyrase subunit A /


Mass: 55537.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3

-
DNA chain , 1 types, 2 molecules EF

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


Mass: 6134.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

-
Non-polymers , 6 types, 342 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-JK8 / (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine


Mass: 364.825 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H17ClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.2 / Details: 11% PEG 5000MME, 150mM BisTris pH6.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.65→58.43 Å / Num. obs: 57152 / % possible obs: 98.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.042 / Rrim(I) all: 0.076 / Net I/σ(I): 12.4
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8352 / Rpim(I) all: 0.36 / Rrim(I) all: 0.645 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2XCS

2xcs


Resolution: 2.65→57.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 21.418 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.264
RfactorNum. reflection% reflectionSelection details
Rfree0.20615 2904 5.1 %RANDOM
Rwork0.16211 ---
obs0.16429 54124 98.38 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 60.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å20 Å2
2---0.46 Å20 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 2.65→57.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10582 807 89 331 11809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01211959
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.60516325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50151360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01821.149653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.975152018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.46615119
X-RAY DIFFRACTIONr_chiral_restr0.1410.21576
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028929
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_it2.643.6265422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2185.4266785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7584.2236537
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.75170.07252290
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B56590.12
12D56590.12
21A156070.1
22C156070.1
31E13970.15
32F13970.15
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 242 -
Rwork0.283 3974 -
obs--98.87 %
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)
11.36860.5357-0.60881.7052-0.32230.27790.0685-0.20570.123-0.0855-0.0140.2337-0.01350.1004-0.05450.28480.03130.01160.165-0.09730.231813.793654.55663.7754
20.2669-0.003-0.03870.3004-0.11830.44220.01310.086-0.11020.09680.02490.0458-0.07710.0447-0.0380.31510.02180.03170.1448-0.03020.255329.820629.099134.3635
33.03661.98431.25192.47210.19510.85010.02750.29-0.40290.27430.1308-0.4139-0.06330.1176-0.15830.33720.02850.01220.0473-0.0060.420728.2484-2.841139.6952
44.67720.1902-0.43230.3774-0.38320.4024-0.2192-0.0925-0.0802-0.06450.0864-0.14420.08-0.08850.13290.39750.00570.01150.0454-0.02090.204110.4554-13.697246.4422
51.1787-0.4008-0.74280.82291.47192.6507-0.1511-0.37390.03550.05840.1853-0.03690.18150.2947-0.03410.37710.05170.00180.2359-0.04350.145333.186447.702161.926
62.0819-1.2517-0.50071.4720.36720.12750.13270.39960.31770.1784-0.0626-0.3183-0.0209-0.0764-0.07010.34440.0278-0.01150.19690.12540.1954-0.446853.835615.4845
70.30890.1174-0.02670.20460.11850.3625-0.0077-0.1138-0.135-0.1465-0.0144-0.0307-0.1032-0.01440.02210.3510.05930.03490.1354-0.01770.2393-19.731933.479946.825
81.1033-1.0634-0.37642.2931-0.28571.95540.054-0.10520.0799-0.147-0.00780.06910.12110.0385-0.04620.34210.01180.0030.0503-0.09930.2982-21.60171.328744.9045
92.0285-0.28590.24010.7110.38740.5565-0.08780.024-0.0838-0.01250.03630.13490.00970.07180.05150.40450.00980.02690.0706-0.05390.1899-5.6633-12.496439.6072
101.2633-0.2765-1.10771.1519-0.882.1387-0.09790.4959-0.01150.1977-0.0299-0.0768-0.0081-0.45540.12780.37210.04720.01270.34930.04280.0317-20.64350.181917.8314
110.5774-0.5434-0.7191.4247-0.04561.5208-0.07370.0402-0.0352-0.08930.0790.10150.0037-0.1696-0.00520.473-0.0367-0.03720.0497-0.02090.240122.111850.89740.5354
121.18980.9057-1.27420.7283-0.84371.84610-0.1090.09170.0348-0.02110.086-0.05950.29180.0210.49370.1260.01090.1432-0.03670.2933-9.885753.689139.1495
130.04030.0119-0.13821.2725-0.14961.7101-0.06410.0337-0.05290.04320.00630.1206-0.2412-0.00740.05780.3962-0.0225-0.00140.153-0.04490.186331.131956.198813.7369
140.44120.58150.44711.24280.22551.2712-0.0201-0.1363-0.063-0.2184-0.1381-0.1436-0.3035-0.0910.15830.42520.02320.01730.1536-0.00310.2157-16.961761.877165.4565
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B417 - 608
2X-RAY DIFFRACTION2A29 - 244
3X-RAY DIFFRACTION2A328 - 369
4X-RAY DIFFRACTION2A461 - 490
5X-RAY DIFFRACTION3A370 - 379
6X-RAY DIFFRACTION3A445 - 460
7X-RAY DIFFRACTION4A380 - 444
8X-RAY DIFFRACTION5A10 - 28
9X-RAY DIFFRACTION5B609 - 638
10X-RAY DIFFRACTION6D417 - 608
11X-RAY DIFFRACTION7C29 - 244
12X-RAY DIFFRACTION7C328 - 369
13X-RAY DIFFRACTION7C461 - 490
14X-RAY DIFFRACTION8C370 - 379
15X-RAY DIFFRACTION8C445 - 460
16X-RAY DIFFRACTION9C380 - 444
17X-RAY DIFFRACTION10C10 - 28
18X-RAY DIFFRACTION10D609 - 638
19X-RAY DIFFRACTION11E1 - 8
20X-RAY DIFFRACTION11F2009 - 2019
21X-RAY DIFFRACTION12E2009 - 2020
22X-RAY DIFFRACTION12F1 - 8
23X-RAY DIFFRACTION13A245 - 327
24X-RAY DIFFRACTION14C245 - 327

+
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://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