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- PDB-5dm7: Crystal structure of the 50S ribosomal subunit from Deinococcus r... -

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Basic information

Entry
Database: PDB / ID: 5dm7
TitleCrystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A
Components
  • (50S ribosomal protein ...) x 28
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / protein synthesis / peptidyltransferase / antibiotic / aminocyclitol
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding ...ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Factor Xa Inhibitor - #60 / Ribosomal protein L1/L10, domain II / Ribosomal protein L1/L10, rRNA-binding domain / Ribosomal protein L25, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, ...Factor Xa Inhibitor - #60 / Ribosomal protein L1/L10, domain II / Ribosomal protein L1/L10, rRNA-binding domain / Ribosomal protein L25, C-terminal domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L25; Chain P / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L6 / Ribosomal Protein L25; Chain P / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / SH3 type barrels. - #30 / Factor Xa Inhibitor / Aldehyde Oxidoreductase; domain 3 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Ribosomal protein L1, bacterial-type / Rubrerythrin, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / RRM (RNA recognition motif) domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Single Sheet / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Beta Complex / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16
Similarity search - Domain/homology
Hygromycin A / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 ...Hygromycin A / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsKaminishi, T. / Schedlbauer, A. / Ochoa-Lizarralde, B. / Connell, S.R. / Fucini, P.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
Authors: Kaminishi, T. / Schedlbauer, A. / Fabbretti, A. / Brandi, L. / Ochoa-Lizarralde, B. / He, C.G. / Milon, P. / Connell, S.R. / Gualerzi, C.O. / Fucini, P.
History
DepositionSep 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: 50S ribosomal protein L1
A: 50S ribosomal protein L2
B: 50S ribosomal protein L3
C: 50S ribosomal protein L4
D: 50S ribosomal protein L5
E: 50S ribosomal protein L6
F: 50S ribosomal protein L11
G: 50S ribosomal protein L13
H: 50S ribosomal protein L14
I: 50S ribosomal protein L15
J: 50S ribosomal protein L16
K: 50S ribosomal protein L17
L: 50S ribosomal protein L18
M: 50S ribosomal protein L19
N: 50S ribosomal protein L20
O: 50S ribosomal protein L21
P: 50S ribosomal protein L22
Q: 50S ribosomal protein L23
R: 50S ribosomal protein L24
S: 50S ribosomal protein L25
T: 50S ribosomal protein L27
U: 50S ribosomal protein L28
V: 50S ribosomal protein L29
W: 50S ribosomal protein L30
Z: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
X: 23S ribosomal RNA
Y: 5S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,360,557217
Polymers1,355,52530
Non-polymers5,032187
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area156000 Å2
ΔGint-1389 kcal/mol
Surface area487040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.820, 411.540, 695.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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50S ribosomal protein ... , 28 types, 28 molecules 0ABCDEFGHIJKLMNOPQRSTUVWZ123

#1: Protein 50S ribosomal protein L1 /


Mass: 23514.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSS8
#2: Protein 50S ribosomal protein L2 /


Mass: 29918.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ9
#3: Protein 50S ribosomal protein L3 /


Mass: 21962.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK2
#4: Protein 50S ribosomal protein L4 /


Mass: 21405.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK1
#5: Protein 50S ribosomal protein L5 /


Mass: 19992.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ0
#6: Protein 50S ribosomal protein L6 /


Mass: 18266.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSL3
#7: Protein 50S ribosomal protein L11 /


Mass: 14945.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSS7
#8: Protein 50S ribosomal protein L13 /


Mass: 15837.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXY1
#9: Protein 50S ribosomal protein L14 /


Mass: 14256.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ2
#10: Protein 50S ribosomal protein L15 /


Mass: 15177.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSK9
#11: Protein 50S ribosomal protein L16 /


Mass: 15543.239 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ5
#12: Protein 50S ribosomal protein L17 /


Mass: 12538.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSJ5
#13: Protein 50S ribosomal protein L18 /


Mass: 11070.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSL2
#14: Protein 50S ribosomal protein L19 /


Mass: 12290.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RWB4
#15: Protein 50S ribosomal protein L20 /


Mass: 13860.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSW7
#16: Protein 50S ribosomal protein L21 /


Mass: 10517.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RY64
#17: Protein 50S ribosomal protein L22 /


Mass: 14432.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ7
#18: Protein 50S ribosomal protein L23 /


Mass: 10336.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK0
#19: Protein 50S ribosomal protein L24 /


Mass: 11770.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ1
#20: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 19184.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RX88
#21: Protein 50S ribosomal protein L27 /


Mass: 8891.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RY65
#22: Protein 50S ribosomal protein L28 /


Mass: 7872.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RRG8
#23: Protein 50S ribosomal protein L29 /


Mass: 7646.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ4
#24: Protein 50S ribosomal protein L30 /


Mass: 6079.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSL0
#25: Protein 50S ribosomal protein L32 /


Mass: 6508.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: P49228
#26: Protein 50S ribosomal protein L33 /


Mass: 5736.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSS4
#27: Protein/peptide 50S ribosomal protein L34 /


Mass: 5626.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSH2
#28: Protein 50S ribosomal protein L35 /


Mass: 7316.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RSW6

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RNA chain , 2 types, 2 molecules XY

#29: RNA chain 23S ribosomal RNA /


Mass: 933750.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 11612676
#30: RNA chain 5S ribosomal RNA /


Mass: 39276.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 11612676

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Non-polymers , 2 types, 187 molecules

#31: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 186 / Source method: obtained synthetically / Formula: Mg
#32: Chemical ChemComp-HGR / Hygromycin A / Totomycin


Mass: 511.476 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29NO12 / Comment: antibiotic*YM

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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: 4.48 Å3/Da / Density % sol: 72.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3→59.03 Å / Num. obs: 479454 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.215 / Net I/σ(I): 6.28
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 5.623 / Mean I/σ(I) obs: 0.33 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→57.02 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 43.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3255 21366 4.83 %
Rwork0.2839 421364 -
obs0.2859 442730 91.9 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.234 Å2 / ksol: 0.208 e/Å3
Displacement parametersBiso max: 401.39 Å2 / Biso mean: 142.3831 Å2 / Biso min: 45.51 Å2
Baniso -1Baniso -2Baniso -3
1--34.6008 Å2-0 Å2-0 Å2
2--66.1499 Å20 Å2
3----31.5491 Å2
Refinement stepCycle: final / Resolution: 3→57.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26865 62274 222 0 89361
Biso mean--93.39 --
Num. residues----6389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00997540
X-RAY DIFFRACTIONf_angle_d1.215145467
X-RAY DIFFRACTIONf_chiral_restr0.07618577
X-RAY DIFFRACTIONf_plane_restr0.0077689
X-RAY DIFFRACTIONf_dihedral_angle_d18.40745406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.03410.50912480.51864998524633
3.0341-3.06980.51922530.49594741499432
3.0698-3.10720.48094700.4905101551062567
3.1072-3.14660.49364930.4895107711126470
3.1466-3.1880.4846420.4842128501349285
3.188-3.23160.47565950.4835132501384587
3.2316-3.27780.48717670.4719146131538096
3.2778-3.32670.50237380.465149591569798
3.3267-3.37870.45967860.4451150111579799
3.3787-3.43410.47137960.43861506515861100
3.4341-3.49330.42237360.42851517815914100
3.4933-3.55680.44457600.41711522415984100
3.5568-3.62520.43317780.39861515615934100
3.6252-3.69920.47187490.4404145391528896
3.6992-3.77960.40247990.354151641596399
3.7796-3.86750.35617600.32911513115891100
3.8675-3.96420.36517500.3207151841593499
3.9642-4.07140.35787860.29191518615972100
4.0714-4.19110.32287820.28651521315995100
4.1911-4.32640.31127810.26541523516016100
4.3264-4.48090.32267540.25471529316047100
4.4809-4.66030.27897920.24231518315975100
4.6603-4.87230.2897750.23661533416109100
4.8723-5.1290.28087870.2291528816075100
5.129-5.45010.2797710.21911532916100100
5.4501-5.87050.26588240.21111530716131100
5.8705-6.46050.27377710.21581539216163100
6.4605-7.39370.26678270.22011538016207100
7.3937-9.30870.27778480.22841543216280100
9.3087-57.0310.25727480.2302158031655199

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