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- PDB-5j5p: AMP-PNP-stabilized ATPase domain of topoisomerase IV from Strepto... -

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Basic information

Entry
Database: PDB / ID: 5j5p
TitleAMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type I
Components
  • DNA (5'-D(*GP*CP*GP*CP*GP*C)-3')
  • DNA topoisomerase 4 subunit BTopoisomerase
KeywordsISOMERASE/DNA / Streptococcus PNEUMONIAE / TOPOISOMERASE IV / DNA BINDING / ISOMERASE / ISOMERASE-DNA COMPLEX / ATPase domain / T-segment
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / DNA topoisomerase, type IIA, subunit B / 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 4 subunit B, Firmicutes/Mollicutes / DNA topoisomerase, type IIA, subunit B / 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 / Ribosomal Protein S5; domain 2 - #10 / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLaponogov, I. / Pan, X.-S. / Skamrova, G. / Umrekar, 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: Nat Commun / Year: 2018
Title: Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase.
Authors: Laponogov, I. / Pan, X.S. / Veselkov, D.A. / Skamrova, G.B. / Umrekar, T.R. / Fisher, L.M. / Sanderson, M.R.
History
DepositionApr 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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

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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
B: DNA topoisomerase 4 subunit B
C: DNA (5'-D(*GP*CP*GP*CP*GP*C)-3')
D: DNA (5'-D(*GP*CP*GP*CP*GP*C)-3')
E: DNA (5'-D(*GP*CP*GP*CP*GP*C)-3')
F: DNA (5'-D(*GP*CP*GP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,46114
Polymers97,3066
Non-polymers1,1568
Water14,844824
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-108 kcal/mol
Surface area33490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.440, 136.460, 136.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / DNA chain , 2 types, 6 molecules ABCDEF

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


Mass: 45032.457 Da / Num. of mol.: 2 / Fragment: ATPase N-terminal domain, residues 1-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: parE, SP_0852 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59961, EC: 5.99.1.3
#2: DNA chain
DNA (5'-D(*GP*CP*GP*CP*GP*C)-3')


Mass: 1810.205 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 4 types, 832 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 824 / 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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M KCl, 10 mM MgCl2, 50 mM Tris-Cl, 30% PEG 400.
Temp details: Incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.91915 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91915 Å / Relative weight: 1
ReflectionResolution: 1.97→45.177 Å / Num. obs: 88222 / % possible obs: 99.79 % / Redundancy: 6.68 % / CC1/2: 0.9904 / Rmerge(I) obs: 0.063 / Net I/σ(I): 6.4
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 7 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: derived from 1EI1
Resolution: 1.97→45.177 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.16
RfactorNum. reflection% reflection
Rfree0.174 4405 4.99 %
Rwork0.1505 --
obs0.1516 88222 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→45.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 480 68 824 7377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176771
X-RAY DIFFRACTIONf_angle_d1.2119294
X-RAY DIFFRACTIONf_dihedral_angle_d24.3612470
X-RAY DIFFRACTIONf_chiral_restr0.4151059
X-RAY DIFFRACTIONf_plane_restr0.0071123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.99240.21661520.19262783X-RAY DIFFRACTION100
1.9924-2.01580.19061540.17832702X-RAY DIFFRACTION100
2.0158-2.04040.18341520.16632798X-RAY DIFFRACTION100
2.0404-2.06620.20021610.16242735X-RAY DIFFRACTION100
2.0662-2.09340.20551610.16772767X-RAY DIFFRACTION100
2.0934-2.12210.19841580.16292736X-RAY DIFFRACTION100
2.1221-2.15240.1871430.16582763X-RAY DIFFRACTION100
2.1524-2.18460.18451410.16052782X-RAY DIFFRACTION100
2.1846-2.21870.16511140.1592812X-RAY DIFFRACTION100
2.2187-2.25510.19881280.15092786X-RAY DIFFRACTION100
2.2551-2.29390.16531430.15092755X-RAY DIFFRACTION100
2.2939-2.33570.20421240.1522825X-RAY DIFFRACTION100
2.3357-2.38060.19031560.15212770X-RAY DIFFRACTION100
2.3806-2.42920.17471500.15142762X-RAY DIFFRACTION100
2.4292-2.4820.18911370.14582787X-RAY DIFFRACTION100
2.482-2.53970.19441700.15012764X-RAY DIFFRACTION100
2.5397-2.60320.17251480.1512793X-RAY DIFFRACTION100
2.6032-2.67360.17861480.162790X-RAY DIFFRACTION100
2.6736-2.75230.18751420.15742765X-RAY DIFFRACTION100
2.7523-2.84110.18391470.15352796X-RAY DIFFRACTION100
2.8411-2.94260.18551680.15772753X-RAY DIFFRACTION100
2.9426-3.06040.18931530.16692815X-RAY DIFFRACTION100
3.0604-3.19960.16491460.16042808X-RAY DIFFRACTION100
3.1996-3.36830.18361440.15912780X-RAY DIFFRACTION100
3.3683-3.57920.16511210.14412847X-RAY DIFFRACTION100
3.5792-3.85550.15131670.13532823X-RAY DIFFRACTION100
3.8555-4.24320.14751260.11882841X-RAY DIFFRACTION100
4.2432-4.85660.10761380.12082845X-RAY DIFFRACTION100
4.8566-6.11640.15681390.15022881X-RAY DIFFRACTION100
6.1164-45.18860.20251740.16472953X-RAY DIFFRACTION99
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)
10.97510.11771.15930.1350.52472.4576-0.0183-0.10980.00820.01180.02250.07730.0293-0.34570.00220.15860.01510.02680.180.03530.188629.690228.88-13.1403
22.2511-0.15280.26292.6443-0.48171.52920.0577-0.28430.5630.1771-0.09160.4721-0.3688-0.03480.03770.21810.070.00310.1207-0.0470.279238.264541.44533.1692
31.9632-0.3590.12541.1763-0.27982.2698-0.046-0.1660.30410.14010.04510.0456-0.2782-0.2242-0.0120.15860.05480.00040.1404-0.02120.169833.225339.5395-0.6356
48.39864.023-4.24384.6215-2.1116.03450.0863-0.0870.12470.0130.0064-0.0346-0.03570.3309-0.08550.12110.0665-0.0080.12140.01480.108148.749828.68727.3699
53.3892-4.3386-1.86876.66061.50111.837-0.3257-0.56450.03610.74650.351-0.11650.57491.0507-0.04840.27240.1254-0.0020.4358-0.00250.211864.96325.84131.5987
65.9874-2.6568-2.17311.59761.14920.7513-0.22340.0567-0.12480.01820.14490.02710.02470.09940.05160.1455-0.001-0.01120.2506-0.01030.155867.013624.6634-14.5679
77.2887-3.23612.51164.2062-1.95164.1303-0.04270.3203-0.0223-0.1087-0.01970.1173-0.13330.18910.0590.14630.00530.04350.1559-0.00890.11251.83333.2402-14.7839
87.1886-5.14544.14014.8394-3.23434.09070.03260.82190.58210.0071-0.0714-0.3615-0.19530.23850.00210.1697-0.03670.04090.32970.03350.198770.918332.8267-16.5336
94.77575.59593.97989.69946.29446.43430.0965-0.1078-0.50460.2803-0.0868-0.33850.5316-0.1592-0.00390.171-0.02910.03610.2727-0.00950.243673.74228.5522-16.161
101.63591.84970.13366.88814.56615.1757-0.47150.0520.01440.42010.26850.25460.12770.23160.15540.15080.04030.02370.12450.03590.183639.352241.1369-6.7566
110.73070.4020.81511.42531.10722.3816-0.05050.03320.18220.01520.0082-0.0178-0.29050.08010.03630.17220.01210.01190.1650.04910.201437.791536.6952-22.6032
122.9086-0.5014-0.53822.07690.10381.5459-0.03850.14170.0653-0.00870.04210.0723-0.0361-0.2035-0.00170.12070.032-0.02520.18260.05650.12525.710727.6249-39.018
130.9921-0.13920.46781.12140.15372.0103-0.07290.05930.0592-0.09810.06030.0817-0.1561-0.14170.01520.12710.02430.01620.14360.04060.145127.462132.8872-35.3458
145.69152.9465-2.35877.7204-2.53446.3343-0.05550.0972-0.0706-0.10180.07340.08020.4146-0.0779-0.0190.11830.06470.02310.13340.02350.119338.617.1155-42.6592
157.3887-4.17611.00123.3015-1.62121.38790.36680.7454-0.0773-0.5519-0.25640.02311.35160.6974-0.12710.52840.17070.02510.3480.0060.228841.61740.8096-36.1492
161.6362-2.80321.46816.0051-3.19141.23260.09630.0386-0.0041-0.0346-0.1497-0.11180.14950.00430.04110.25590.0131-0.00560.1644-0.00510.165741.4984-0.5766-19.524
173.0909-3.2664-0.85976.81991.59813.0449-0.0894-0.0990.01430.24350.0107-0.14820.19180.01940.08140.16760.0189-0.00540.1520.0570.116933.339214.6526-20.346
185.5441-4.9086-2.97214.27982.96982.7278-0.067-0.0916-0.43130.48530.19970.75770.0397-0.1606-0.13850.35120.00210.00120.1820.06430.251533.6066-4.132-17.7984
199.59675.15176.49094.70123.9477.54850.07230.0376-0.2391-0.00040.012-0.3937-0.07730.3229-0.11180.2354-0.00830.00210.1520.01340.235757.4331-7.3838-17.244
203.16961.71453.25941.41651.88263.56930.09530.15770.03070.1668-0.24980.12850.1924-0.04430.13570.11370.00990.03070.18870.06910.210525.732226.8426-29.0358
212.27673.2424-0.96035.0832-3.21188.4942-0.0575-0.50950.6335-0.5628-0.38510.2545-0.82310.78590.52930.7745-0.07330.01820.3712-0.01090.570145.2937.119-7.7122
223.02141.1693-3.37829.72482.46859.317-1.0416-0.28630.04420.23340.17210.4261-0.56760.62410.8370.81460.0309-0.03540.52850.04110.507744.99368.004-1.0954
232.6351.61491.21268.67471.23338.5107-0.2954-0.48640.9485-0.3472-0.3810.7830.6614-0.35540.70410.3809-0.0671-0.01950.8690.01080.697859.859120.7544-26.6894
249.46860.99571.79842.5441-4.03549.1470.1211-0.06650.64750.119-1.1765-0.1530.58771.03360.94690.842-0.0478-0.06111.12240.04960.556559.168320.9328-33.4301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 189 )
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 245 )
6X-RAY DIFFRACTION6chain 'A' and (resid 246 through 323 )
7X-RAY DIFFRACTION7chain 'A' and (resid 324 through 349 )
8X-RAY DIFFRACTION8chain 'A' and (resid 350 through 371 )
9X-RAY DIFFRACTION9chain 'A' and (resid 372 through 400 )
10X-RAY DIFFRACTION10chain 'A' and resid 800
11X-RAY DIFFRACTION11chain 'B' and (resid 5 through 57 )
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 93 )
13X-RAY DIFFRACTION13chain 'B' and (resid 94 through 189 )
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 222 )
15X-RAY DIFFRACTION15chain 'B' and (resid 223 through 245 )
16X-RAY DIFFRACTION16chain 'B' and (resid 246 through 323 )
17X-RAY DIFFRACTION17chain 'B' and (resid 324 through 349 )
18X-RAY DIFFRACTION18chain 'B' and (resid 350 through 371 )
19X-RAY DIFFRACTION19chain 'B' and (resid 372 through 400 )
20X-RAY DIFFRACTION20chain 'B' and resid 800
21X-RAY DIFFRACTION21chain 'C'
22X-RAY DIFFRACTION22chain 'D'
23X-RAY DIFFRACTION23chain 'E'
24X-RAY DIFFRACTION24chain 'F'

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