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- PDB-5iwe: E45Q mutant of phenazine biosynthesis protein PhzF in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5iwe
TitleE45Q mutant of phenazine biosynthesis protein PhzF in complex with (5R,6R)-6-azaniumyl-5-ethoxycyclohexa-1,3-diene-1-carboxylate
ComponentsTrans-2,3-dihydro-3-hydroxyanthranilate isomerase
KeywordsISOMERASE / complex / substrate analogue
Function / homology
Function and homology information


trans-2,3-dihydro-3-hydroxyanthranilate isomerase / trans-2,3-dihydro-3-hydroxy-anthranilate isomerase activity / phenazine biosynthetic process / cytoplasm
Similarity search - Function
Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-W81 / Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsDiederich, C. / Blankenfeldt, W.
Funding support Germany, Austria, 2items
OrganizationGrant numberCountry
ERA-Chemistry networkBL587-3 Germany
ERA-Chemistry networkI-668 Austria
CitationJournal: Sci Rep / Year: 2017
Title: Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF.
Authors: Diederich, C. / Leypold, M. / Culka, M. / Weber, H. / Breinbauer, R. / Ullmann, G.M. / Blankenfeldt, W.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: 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 / _citation_author.name
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9598
Polymers32,2561
Non-polymers7047
Water4,360242
1
A: Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
hetero molecules

A: Trans-2,3-dihydro-3-hydroxyanthranilate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,91916
Polymers64,5112
Non-polymers1,40814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)56.032, 56.032, 155.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

21A-569-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Trans-2,3-dihydro-3-hydroxyanthranilate isomerase / Phenazine/pyocyanine biosynthesis protein PhzF


Mass: 32255.576 Da / Num. of mol.: 1 / Mutation: E45Q
Source method: isolated from a genetically manipulated source
Details: The first 19 residues consist of the N-terminal expression tag and are neither natural nor visible in the structure
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: phzF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 (pLysS)
References: UniProt: Q51792, trans-2,3-dihydro-3-hydroxyanthranilate isomerase

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Non-polymers , 5 types, 249 molecules

#2: Chemical ChemComp-W81 / (5R,6R)-6-azaniumyl-5-ethoxycyclohexa-1,3-diene-1-carboxylate


Mass: 183.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.085M sodium acetate pH 4.6, 0.17M ammonium acetate, 25.5% (w/v) PEG 4000, 15% (v/v) glycerol, temperature 293.15K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2015
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.71→77.87 Å / Num. obs: 31593 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.9
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSv.052data reduction
Aimless0.5.17data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U1V
Resolution: 1.71→46.328 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.89 / Details: TLS-refinement
RfactorNum. reflection% reflection
Rfree0.1734 1612 5.11 %
Rwork0.1492 --
obs0.1505 31532 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.71→46.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 47 242 2413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072270
X-RAY DIFFRACTIONf_angle_d0.9453083
X-RAY DIFFRACTIONf_dihedral_angle_d11.6581367
X-RAY DIFFRACTIONf_chiral_restr0.059340
X-RAY DIFFRACTIONf_plane_restr0.007411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.76040.2721390.23782457X-RAY DIFFRACTION100
1.7604-1.81720.21651260.20012441X-RAY DIFFRACTION100
1.8172-1.88210.19471340.18192453X-RAY DIFFRACTION100
1.8821-1.95750.21481340.17282440X-RAY DIFFRACTION100
1.9575-2.04660.17141400.1472458X-RAY DIFFRACTION100
2.0466-2.15450.19221250.13772481X-RAY DIFFRACTION100
2.1545-2.28950.17651380.13692440X-RAY DIFFRACTION100
2.2895-2.46620.16181310.12822504X-RAY DIFFRACTION100
2.4662-2.71440.1741250.12752505X-RAY DIFFRACTION100
2.7144-3.10710.13981250.12732536X-RAY DIFFRACTION100
3.1071-3.91430.15271510.12552521X-RAY DIFFRACTION100
3.9143-46.34550.1681440.17072684X-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)
11.5929-0.74580.26211.0797-0.14271.3181-0.0132-0.0143-0.0026-0.0326-0.00160.0308-0.1524-0.08540.01660.1168-0.0064-0.00310.09180.01130.07315.766634.41727.1087
20.81590.63770.90721.78562.20313.8872-0.0122-0.03420.0148-0.0531-0.00490.1271-0.1589-0.20440.0450.1085-0.00280.01370.12330.01910.11819.892734.131117.1868
33.2181-0.0582-0.17161.43780.99992.65380.0547-0.11050.23490.1020.0253-0.1216-0.1113-0.0212-0.08160.1298-0.0023-0.02210.08810.02690.117220.643435.696720.7601
40.4222-0.1417-0.06270.8727-0.34970.3888-0.0238-0.00830.04020.00960.02730.1554-0.01870.01150.00280.0907-0.0007-0.00420.08580.00660.084517.262216.491220.9822
54.9578-1.58130.29182.4451-0.47661.85250.10470.42230.0832-0.5336-0.05640.1580.0997-0.1193-0.02570.2107-0.028-0.04460.09340.01250.130515.22295.42229.4622
60.2095-0.709-0.05182.6766-0.03373.1746-0.07010.02290.0032-0.1243-0.0136-0.1205-0.04020.15520.09230.1206-0.00570.00820.08260.02860.090924.766810.210916.8686
70.6802-0.0002-0.44561.5482-0.49910.83470.02780.0609-0.0008-0.1518-0.02160.0109-0.04880.0097-0.01890.1181-0.0013-0.00580.06910.00290.082121.613314.088218.2896
80.5644-0.1545-0.24012.1215-1.34661.5252-0.0342-0.075-0.06620.1908-0.1033-0.0438-0.11550.11550.11040.1096-0.0293-0.02380.0897-0.01420.085923.29725.734220.8457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 50 )) or ( chain 'B' and resid 2 ) or ( chain 'B' and resid 12 ) or ( chain 'B' and resid 14 ) or ( chain 'B' and resid 20 ) or ( chain 'B' and resid 28 ) or ( chain 'B' and resid 30 ) or ( chain 'B' and resid 32 ) or ( chain 'B' and resid 35 ) or ( chain 'B' and resid 37 ) or ( chain 'B' and resid 39 ) or ( chain 'B' and resid 43 ) or ( chain 'B' and resid 51 ) or ( chain 'B' and resid 62 ) or ( chain 'B' and resid 70 ) or ( chain 'B' and resid 72 ) or ( chain 'B' and resid 73 ) or ( chain 'B' and resid 102 ) or ( chain 'B' and resid 104 ) or ( chain 'B' and resid 108 ) or ( chain 'B' and resid 110 ) or ( chain 'B' and resid 111 ) or ( chain 'B' and resid 112 ) or ( chain 'B' and resid 121 ) or ( chain 'B' and resid 124 ) or ( chain 'B' and resid 125 ) or ( chain 'B' and resid 127 ) or ( chain 'B' and resid 134 ) or ( chain 'B' and resid 138 ) or ( chain 'B' and resid 141 ) or ( chain 'B' and resid 142 ) or ( chain 'B' and resid 158 ) or ( chain 'B' and resid 159 ) or ( chain 'B' and resid 160 ) or ( chain 'B' and resid 162 ) or ( chain 'B' and resid 163 ) or ( chain 'B' and resid 164 ) or ( chain 'B' and resid 165 ) or ( chain 'B' and resid 166 ) or ( chain 'B' and resid 167 ) or ( chain 'B' and resid 168 ) or ( chain 'B' and resid 220 ) or ( chain 'B' and resid 223 ) or ( chain 'B' and resid 241 ) or ( chain 'B' and resid 242 ) or ( chain 'D' and resid 2 ))
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 72 )) or ( chain 'B' and resid 5 ) or ( chain 'B' and resid 24 ) or ( chain 'B' and resid 25 ) or ( chain 'B' and resid 31 ) or ( chain 'B' and resid 38 ) or ( chain 'B' and resid 56 ) or ( chain 'B' and resid 67 ) or ( chain 'B' and resid 84 ) or ( chain 'B' and resid 105 ) or ( chain 'B' and resid 114 ) or ( chain 'B' and resid 126 ) or ( chain 'B' and resid 128 ) or ( chain 'B' and resid 129 ) or ( chain 'B' and resid 131 ) or ( chain 'B' and resid 132 ) or ( chain 'B' and resid 133 ) or ( chain 'B' and resid 146 ) or ( chain 'B' and resid 169 ) or ( chain 'B' and resid 170 ) or ( chain 'B' and resid 171 ) or ( chain 'B' and resid 172 ) or ( chain 'B' and resid 177 ) or ( chain 'B' and resid 178 ) or ( chain 'B' and resid 180 ) or ( chain 'B' and resid 183 ) or ( chain 'B' and resid 229 ) or ( chain 'B' and resid 230 ) or ( chain 'E' and resid 1 ))
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 98 )) or ( chain 'B' and resid 68 ) or ( chain 'B' and resid 69 ) or ( chain 'B' and resid 89 ) or ( chain 'B' and resid 91 ) or ( chain 'B' and resid 99 ) or ( chain 'B' and resid 103 ) or ( chain 'B' and resid 116 ) or ( chain 'B' and resid 179 ) or ( chain 'B' and resid 189 ) or ( chain 'B' and resid 190 ) or ( chain 'B' and resid 191 ) or ( chain 'B' and resid 204 ) or ( chain 'B' and resid 233 ) or ( chain 'B' and resid 234 ) or ( chain 'B' and resid 237 ) or ( chain 'B' and resid 239 ) or ( chain 'E' and resid 2 ))
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 159 )) or ( chain 'B' and resid 1 ) or ( chain 'B' and resid 3 ) or ( chain 'B' and resid 15 ) or ( chain 'B' and resid 16 ) or ( chain 'B' and resid 21 ) or ( chain 'B' and resid 23 ) or ( chain 'B' and resid 26 ) or ( chain 'B' and resid 29 ) or ( chain 'B' and resid 34 ) or ( chain 'B' and resid 36 ) or ( chain 'B' and resid 40 ) or ( chain 'B' and resid 41 ) or ( chain 'B' and resid 42 ) or ( chain 'B' and resid 47 ) or ( chain 'B' and resid 48 ) or ( chain 'B' and resid 49 ) or ( chain 'B' and resid 52 ) or ( chain 'B' and resid 53 ) or ( chain 'B' and resid 57 ) or ( chain 'B' and resid 58 ) or ( chain 'B' and resid 59 ) or ( chain 'B' and resid 64 ) or ( chain 'B' and resid 71 ) or ( chain 'B' and resid 76 ) or ( chain 'B' and resid 81 ) or ( chain 'B' and resid 83 ) or ( chain 'B' and resid 92 ) or ( chain 'B' and resid 93 ) or ( chain 'B' and resid 101 ) or ( chain 'B' and resid 118 ) or ( chain 'B' and resid 130 ) or ( chain 'B' and resid 137 ) or ( chain 'B' and resid 139 ) or ( chain 'B' and resid 144 ) or ( chain 'B' and resid 145 ) or ( chain 'B' and resid 150 ) or ( chain 'B' and resid 151 ) or ( chain 'B' and resid 156 ) or ( chain 'B' and resid 181 ) or ( chain 'B' and resid 182 ) or ( chain 'B' and resid 185 ) or ( chain 'B' and resid 188 ) or ( chain 'B' and resid 192 ) or ( chain 'B' and resid 193 ) or ( chain 'B' and resid 194 ) or ( chain 'B' and resid 195 ) or ( chain 'B' and resid 196 ) or ( chain 'B' and resid 197 ) or ( chain 'B' and resid 198 ) or ( chain 'B' and resid 199 ) or ( chain 'B' and resid 201 ) or ( chain 'B' and resid 203 ) or ( chain 'B' and resid 226 ) or ( chain 'B' and resid 228 ) or ( chain 'B' and resid 231 ) or ( chain 'B' and resid 232 ) or ( chain 'B' and resid 235 ) or ( chain 'B' and resid 238 ) or ( chain 'B' and resid 240 ) or ( chain 'D' and resid 1 ) or ( chain 'F' and resid 1 ))
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 182 )) or ( chain 'B' and resid 10 ) or ( chain 'B' and resid 27 ) or ( chain 'B' and resid 44 ) or ( chain 'B' and resid 54 ) or ( chain 'B' and resid 74 ) or ( chain 'B' and resid 79 ) or ( chain 'B' and resid 86 ) or ( chain 'B' and resid 87 ) or ( chain 'B' and resid 95 ) or ( chain 'B' and resid 97 ) or ( chain 'B' and resid 119 ) or ( chain 'B' and resid 122 ) or ( chain 'B' and resid 135 ) or ( chain 'B' and resid 136 ) or ( chain 'B' and resid 148 ) or ( chain 'B' and resid 153 ) or ( chain 'B' and resid 154 ) or ( chain 'B' and resid 155 ) or ( chain 'B' and resid 157 ) or ( chain 'B' and resid 200 ) or ( chain 'B' and resid 202 ) or ( chain 'B' and resid 206 ) or ( chain 'B' and resid 207 ) or ( chain 'B' and resid 211 ) or ( chain 'B' and resid 212 ) or ( chain 'B' and resid 213 ))
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 199 )) or ( chain 'B' and resid 6 ) or ( chain 'B' and resid 7 ) or ( chain 'B' and resid 8 ) or ( chain 'B' and resid 11 ) or ( chain 'B' and resid 55 ) or ( chain 'B' and resid 78 ) or ( chain 'B' and resid 80 ) or ( chain 'B' and resid 82 ) or ( chain 'B' and resid 106 ) or ( chain 'B' and resid 117 ) or ( chain 'B' and resid 147 ) or ( chain 'B' and resid 152 ) or ( chain 'B' and resid 205 ) or ( chain 'B' and resid 224 ))
7X-RAY DIFFRACTION7chain 'A' and (resid 200 through 245 )) or ( chain 'B' and resid 4 ) or ( chain 'B' and resid 17 ) or ( chain 'B' and resid 22 ) or ( chain 'B' and resid 45 ) or ( chain 'B' and resid 50 ) or ( chain 'B' and resid 65 ) or ( chain 'B' and resid 77 ) or ( chain 'B' and resid 85 ) or ( chain 'B' and resid 90 ) or ( chain 'B' and resid 94 ) or ( chain 'B' and resid 98 ) or ( chain 'B' and resid 113 ) or ( chain 'B' and resid 115 ) or ( chain 'B' and resid 123 ) or ( chain 'B' and resid 143 ) or ( chain 'B' and resid 173 ) or ( chain 'B' and resid 174 ) or ( chain 'B' and resid 175 ) or ( chain 'B' and resid 176 ) or ( chain 'B' and resid 208 ) or ( chain 'B' and resid 209 ) or ( chain 'B' and resid 210 ) or ( chain 'B' and resid 214 ) or ( chain 'B' and resid 215 ) or ( chain 'B' and resid 216 ) or ( chain 'B' and resid 227 ) or ( chain 'C' and resid 1 ))
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 278 )) or ( chain 'B' and resid 9 ) or ( chain 'B' and resid 13 ) or ( chain 'B' and resid 18 ) or ( chain 'B' and resid 19 ) or ( chain 'B' and resid 33 ) or ( chain 'B' and resid 46 ) or ( chain 'B' and resid 60 ) or ( chain 'B' and resid 61 ) or ( chain 'B' and resid 63 ) or ( chain 'B' and resid 66 ) or ( chain 'B' and resid 75 ) or ( chain 'B' and resid 88 ) or ( chain 'B' and resid 96 ) or ( chain 'B' and resid 100 ) or ( chain 'B' and resid 107 ) or ( chain 'B' and resid 109 ) or ( chain 'B' and resid 120 ) or ( chain 'B' and resid 140 ) or ( chain 'B' and resid 149 ) or ( chain 'B' and resid 161 ) or ( chain 'B' and resid 184 ) or ( chain 'B' and resid 186 ) or ( chain 'B' and resid 187 ) or ( chain 'B' and resid 217 ) or ( chain 'B' and resid 218 ) or ( chain 'B' and resid 219 ) or ( chain 'B' and resid 221 ) or ( chain 'B' and resid 222 ) or ( chain 'B' and resid 225 ) or ( chain 'B' and resid 236 ))

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