[English] 日本語
Yorodumi
- PDB-6y2p: Escherichia coli RnlA-RnlB Toxin-Antitoxin System. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y2p
TitleEscherichia coli RnlA-RnlB Toxin-Antitoxin System.
Components
  • Antitoxin RnlB
  • mRNA endoribonuclease toxin LS
KeywordsTOXIN / Prokaryotic Toxin-Antitoxin System / Endoribonuclease / HEPN protein / T4 phage denfense / Antitoxin
Function / homology
Function and homology information


toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / protein homodimerization activity / cytoplasm
Similarity search - Function
Antitoxin RnlB/LsoB / Antitoxin to bacterial toxin RNase LS or RnlA / Bacterial toxin RNase RnlA/LsoA, N repeated domain / Bacterial toxin RNase RnlA/LsoA, N-terminal domain / Bacterial toxin, RNase RnlA/LsoA, N-terminal repeated domain / Bacterial toxin, RNase RnlA/LsoA, DBD domain / Bacterial toxin, RNase RnlA/LsoA, N-terminal / RNase LS, bacterial toxin / RNase LS, bacterial toxin DBD domain / RNase LS, bacterial toxin N-terminal ...Antitoxin RnlB/LsoB / Antitoxin to bacterial toxin RNase LS or RnlA / Bacterial toxin RNase RnlA/LsoA, N repeated domain / Bacterial toxin RNase RnlA/LsoA, N-terminal domain / Bacterial toxin, RNase RnlA/LsoA, N-terminal repeated domain / Bacterial toxin, RNase RnlA/LsoA, DBD domain / Bacterial toxin, RNase RnlA/LsoA, N-terminal / RNase LS, bacterial toxin / RNase LS, bacterial toxin DBD domain / RNase LS, bacterial toxin N-terminal / TATA-Binding Protein / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
mRNA endoribonuclease toxin LS / Antitoxin RnlB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsGarcia-Rodriguez, G. / Talavera Perez, A. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0B25.15N Belgium
Citation
Journal: Nucleic Acids Res. / Year: 2021
Title: Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA.
Authors: Garcia-Rodriguez, G. / Charlier, D. / Wilmaerts, D. / Michiels, J. / Loris, R.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2020
Title: The Escherichia coli RnlA-RnlB toxin-antitoxin complex: production, characterization and crystallization.
Authors: Garcia-Rodriguez, G. / Talavera Perez, A. / Konijnenberg, A. / Sobott, F. / Michiels, J. / Loris, R.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: mRNA endoribonuclease toxin LS
B: mRNA endoribonuclease toxin LS
C: Antitoxin RnlB
D: Antitoxin RnlB


Theoretical massNumber of molelcules
Total (without water)110,1284
Polymers110,1284
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Isolated RnlA is present as a dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-50 kcal/mol
Surface area40330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.320, 133.580, 55.640
Angle α, β, γ (deg.)90.000, 95.110, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...
21(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC11
12GLYGLYGLYGLY(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1111
13GLUGLUGLUGLU(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC4747
14METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
15METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
16METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
17METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
18METMETSERSER(CHAIN C AND (RESID 1 THROUGH 7 OR RESID 11...CC1 - 1201 - 120
21METMETMETMET(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD11
22GLYGLYGLYGLY(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1111
23LYSLYSLYSLYS(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1414
24METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120
25METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120
26METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120
27METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120
28METMETSERSER(CHAIN D AND (RESID 1 THROUGH 7 OR RESID 11...DD1 - 1201 - 120

-
Components

#1: Protein mRNA endoribonuclease toxin LS / RNase LS / Toxin LS


Mass: 40104.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rnlA, std, yfjN, b2630, JW2611 / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52129, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin RnlB


Mass: 14960.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rnlB, yfjO, b2631, JW5418 / Plasmid: pET28a
Details (production host): It was expressed as the rnlAB operon cloned into pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52130
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein Buffer: 20 mM Tris HCl pH 8, 150 mM NaCl, 1 mM tris (2-carboxyethyl) phosphine. Reservoir solution: 0.1 M Tris HCl pH 8.5, 25 % (w/v) SOKALAN CP 5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980073 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980073 Å / Relative weight: 1
ReflectionResolution: 2.64→48.78 Å / Num. obs: 51657 / % possible obs: 99.2 % / Redundancy: 6.77 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.1
Reflection shellResolution: 2.64→2.73 Å / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 4871

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MR-Rosettaphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8O

4i8o


Resolution: 2.64→48.78 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.68
RfactorNum. reflection% reflection
Rfree0.242 2576 4.99 %
Rwork0.197 49010 -
obs0.199 51586 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 237.75 Å2 / Biso mean: 96.03 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.64→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6975 0 0 27 7002
Biso mean---66.23 -
Num. residues----943
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C688X-RAY DIFFRACTIONPOSITIONAL0
12D688X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.64-2.690.30541180.30182291240985
2.69-2.740.27651450.25327532898100
2.74-2.80.27821440.255227322876100
2.8-2.870.30181430.263927142857100
2.87-2.940.36651470.29227842931100
2.94-3.020.2881420.257927002842100
3.02-3.110.30261450.246827462891100
3.11-3.210.32071440.233327382882100
3.21-3.320.30011440.235727262870100
3.32-3.460.26711450.224527662911100
3.46-3.610.23831440.212827222866100
3.61-3.810.24041440.186927602904100
3.81-4.040.21451450.170927642909100
4.04-4.360.211440.163227302874100
4.36-4.790.19311450.159627542899100
4.79-5.490.2251450.178427572902100
5.49-6.910.28521460.215127772923100
6.91-48.780.20511460.16962796294299
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)
15.8736-3.2352-2.69497.43025.71136.9317-0.59990.823-1.3628-0.59570.34490.26630.9726-0.28110.54041.054-0.21080.1560.5859-0.09551.255372.351-27.309155.1919
26.9699-3.0655-3.51866.41345.87456.7531-0.58860.0112-1.2875-0.41120.7737-1.24140.6730.67880.00971.26080.03060.27170.7307-0.04321.69881.2051-31.750655.0763
32.55851.03310.32876.4865-0.1682.0231-0.1885-0.0232-0.66790.44270.11390.46410.4983-0.09150.18720.9011-0.22280.02490.5641-0.01490.748765.5539-19.151463.0201
44.03640.7091-1.12772.71310.02352.2183-0.2393-1.4527-0.881.8216-0.88740.88981.38030.53420.35992.377-0.25870.58021.06480.21161.219458.9193-25.131881.3105
53.57050.6666-1.74482.95050.47493.3223-0.4469-0.6051-0.50592.24440.27230.6890.72140.33860.52191.5962-0.10630.24090.8330.10161.042262.0948-19.80675.6713
62.30170.7324-1.35191.9426-1.0082.2559-0.48340.5705-0.46660.62180.12111.48450.9202-0.48640.23370.9626-0.26770.25160.7863-0.18311.229156.6376-14.044966.4663
72.522-0.2839-0.97921.9782-0.42071.97860.0910.2511-0.3933-0.2299-0.20610.18210.2873-0.3412-0.02340.4415-0.0869-0.08370.6228-0.06420.366478.305-0.699948.3633
82.5970.0925-1.85534.83922.69852.9302-0.0526-0.0006-0.18750.00360.23660.3048-0.84190.7034-0.30020.7417-0.05130.0121.0337-0.00110.380192.0379.982931.2178
91.5072-1.3609-2.5073.13163.74098.7801-0.26050.66590.1545-0.31260.21730.4361-0.32640.2928-0.07190.49750.0043-0.06810.72570.01950.397483.300210.464937.1332
101.487-0.2528-0.51462.29471.81175.1282-0.09530.31130.0422-0.3132-0.12950.3091-0.1344-0.67660.25050.44380.0124-0.07910.57460.01810.390277.437211.079347.3116
115.8491-6.606-0.21837.40730.15721.8535-0.5962-0.7302-0.70571.18730.52531.8043-1.7992-0.6875-0.07162.00290.170.33580.9544-0.0761.997841.008313.718780.0104
128.5672-0.3494-1.53936.35211.46467.1931-0.2751.65040.4753-1.2042-0.20082.4842-0.3589-1.39840.44571.0028-0.0521-0.46221.0892-0.0411.570547.9725-1.674156.0229
132.2389-0.11890.06422.29150.35452.62780.0161-0.1680.22230.185-0.0288-0.1082-0.2070.1744-0.01010.4233-0.0699-0.05160.5037-0.0240.300188.878212.095263.142
146.5938-1.9065-4.00845.0856.22238.0947-0.4934-0.09050.7375-0.7241.1485-0.3225-2.4413-1.4574-0.49631.48720.2320.0840.79220.21420.820579.58936.947242.3324
158.2642-0.1779-2.01833.1575-3.06513.5496-0.28470.08772.0683-0.8682-0.5273-0.2867-2.3672-0.63080.36881.53830.4927-0.2950.71680.02031.195976.323642.127348.832
165.8764.77230.17848.14995.74187.7011-0.07180.41390.17-1.13120.2619-0.9725-1.10110.28930.06490.74750.09740.06280.63630.13260.59683.944826.997445.1301
173.06464.3529-0.05757.60981.67192.1658-0.24380.8421.6242-1.97520.8222-0.8054-1.8960.5363-0.1551.2696-0.04840.19390.82880.17991.100488.275140.335345.8628
183.87213.70713.2553.69592.46826.1430.33510.36982.00611.0358-0.31790.4257-1.54340.4633-0.18941.42450.0649-0.16350.678-0.01361.251681.380841.955851.6332
198.20963.23582.21272.1127-0.03576.48160.0966-0.41950.9391-0.6122-0.41430.7612-1.0453-0.71790.32570.69750.2383-0.02310.596-0.02330.624575.846128.735652.3511
204.9890.3083-3.63975.38664.82267.53730.1061-0.02362.17320.91540.6576-0.7-2.0587-0.0097-0.46691.53480.0972-0.24170.57420.0481.130584.436137.497258.0375
213.5508-4.5093-1.64635.88162.80934.1236-0.7515-0.6304-0.09741.433-0.15921.0923-1.3988-2.17750.91770.9930.4276-0.03391.0559-0.15281.19866.518334.060455.6141
223.8006-1.7179-1.25928.88225.75957.1950.20090.20670.5215-1.25-0.39580.9758-1.4325-0.75920.36120.84860.358-0.14150.96480.06690.779470.578630.393139.8897
231.7422.586-2.04994.2778-3.82923.83340.60270.11162.2923-0.66170.47643.29260.2146-1.4346-0.90010.8280.0958-0.30591.4963-0.04951.693464.613421.559641.7917
248.1006-5.0338-4.88826.51834.04777.09940.010.4111-0.466-0.51850.3865-0.1145-0.11660.9103-0.43260.4792-0.1014-0.11150.7627-0.09360.5373108.4729-6.448446.1434
256.2318-4.3245-3.6989.13084.87293.13840.03490.7504-0.585-0.31760.1173-0.29940.22870.1115-0.05770.5545-0.0508-0.06030.7031-0.10320.5507101.3925-10.010148.2111
267.0791-0.8308-0.38168.64451.83227.1979-0.05551.1028-0.9855-0.31-0.0486-0.0384-0.039-0.4218-0.17640.4234-0.0678-0.06250.7461-0.27950.618399.0963-13.494844.3782
278.50662.71552.98574.57742.9148.87290.3162-0.2416-0.63440.17690.0627-0.73180.16710.9921-0.47540.4380.0053-0.04310.62710.07530.4142108.5045-7.17960.7269
289.0172-5.841-5.36863.82153.23484.772-1.0425-1.797-1.65421.76580.27930.20851.76731.43081.00231.15490.05010.00221.0240.08510.6042101.4174-6.365768.7387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 26 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 27 THROUGH 77 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 78 THROUGH 113 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 114 THROUGH 143 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 144 THROUGH 169 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 170 THROUGH 203 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 204 THROUGH 267 )A0
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 268 THROUGH 300 )A0
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 301 THROUGH 321 )A0
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 322 THROUGH 357 )A0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 4 THROUGH 99 )B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 100 THROUGH 189 )B0
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 190 THROUGH 357 )B0
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 1 THROUGH 7 )C0
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 8 THROUGH 19 )C0
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 20 THROUGH 28 )C0
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 29 THROUGH 39 )C0
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 40 THROUGH 51 )C0
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 52 THROUGH 68 )C0
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 69 THROUGH 81 )C0
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 82 THROUGH 87 )C0
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 88 THROUGH 111 )C0
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 112 THROUGH 120 )C0
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 1 THROUGH 39 )D0
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 40 THROUGH 68 )D0
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 69 THROUGH 87 )D0
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 88 THROUGH 111 )D0
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 112 THROUGH 120 )D0

+
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