[English] 日本語
Yorodumi
- PDB-7p6j: Crystal structure of glycosyl-enzyme intermediate of RBcel1 Y201F -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p6j
TitleCrystal structure of glycosyl-enzyme intermediate of RBcel1 Y201F
ComponentsEndoglucanase
KeywordsHYDROLASE / Transglycosylase / GH5_5 family / complex / glycosyl-enzyme intermediate
Function / homology
Function and homology information


glucan catabolic process / cellulase / cellulase activity
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-cellobiose / beta-cellotetraose / alpha-cellotriose / beta-D-glucopyranose / Endoglucanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsCollet, L. / Dutoit, R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Highlighting the factors governing transglycosylation in the GH5_5 endo-1,4-beta-glucanase RBcel1.
Authors: Collet, L. / Vander Wauven, C. / Oudjama, Y. / Galleni, M. / Dutoit, R.
History
DepositionJul 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
C: Endoglucanase
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,00413
Polymers145,4644
Non-polymers4,5409
Water20,8791159
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3753
Polymers36,3661
Non-polymers1,0092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6993
Polymers36,3661
Non-polymers1,3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5373
Polymers36,3661
Non-polymers1,1712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3934
Polymers36,3661
Non-polymers1,0273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.560, 90.540, 89.680
Angle α, β, γ (deg.)90.000, 118.770, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Non-polymers , 2 types, 1163 molecules ABCD

#1: Protein
Endoglucanase


Mass: 36366.051 Da / Num. of mol.: 4 / Mutation: Y201F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pBAD-TOPO / Production host: Escherichia coli MC1061 (bacteria) / Strain (production host): MC1061 / References: UniProt: C1JI15, cellulase
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1159 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 6 types, 9 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Reservoir: 0.1M Tris, 21% PEG600, pH7 Protein-ligand mix: 100 ul protein (14.1 mg/ml in 20 mM sodium phosphate buffer pH6.5) + 36 ul 212 mM cellotriose. Drop: 2 ul reservoir + 2 ul protein- ...Details: Reservoir: 0.1M Tris, 21% PEG600, pH7 Protein-ligand mix: 100 ul protein (14.1 mg/ml in 20 mM sodium phosphate buffer pH6.5) + 36 ul 212 mM cellotriose. Drop: 2 ul reservoir + 2 ul protein-ligand mix + 0.2 ul microseeds.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→44.82 Å / Num. obs: 124776 / % possible obs: 98.8 % / Redundancy: 6.78 % / Biso Wilson estimate: 28.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.073 / Χ2: 1.088 / Net I/σ(I): 13.54 / Num. measured all: 845927
Reflection shellResolution: 1.75→44.82 Å / Redundancy: 6.23 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.57 / Num. measured obs: 9542 / Num. possible: 1498 / Num. unique obs: 1467 / CC1/2: 0.998 / Rrim(I) all: 0.037 / % possible all: 93.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.77 Å44.82 Å
Translation2.77 Å44.82 Å

-
Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDS20190315data reduction
XSCALE20190315data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EE9

4ee9


Resolution: 1.75→44.82 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 6235 5 %
Rwork0.172 118499 -
obs0.174 124734 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.4 Å2 / Biso mean: 37.47 Å2 / Biso min: 16.31 Å2
Refinement stepCycle: final / Resolution: 1.75→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10202 0 302 1159 11663
Biso mean--37.02 41.4 -
Num. residues----1274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.760.48021790.42213399357886
1.76-1.790.35782050.3543922412799
1.79-1.810.37742090.33183974418399
1.81-1.830.32442060.3083912411899
1.83-1.850.28772090.27043953416299
1.85-1.880.28152050.23713908411399
1.88-1.910.2522060.223911411799
1.91-1.940.25652090.21143954416399
1.94-1.970.25092080.20873956416499
1.97-20.25512070.20673939414699
2-2.030.26172080.20023940414899
2.03-2.070.25282100.1933991420199
2.07-2.110.23462090.19373965417499
2.11-2.150.25032080.20043949415799
2.15-2.20.22712080.20239544162100
2.2-2.250.21452080.186239684176100
2.25-2.310.19852080.169939494157100
2.31-2.370.19272090.171639654174100
2.37-2.440.20922090.171839984207100
2.44-2.520.20962100.179239714181100
2.52-2.610.19252090.174539804189100
2.61-2.710.20892090.178839674176100
2.71-2.830.20882100.186640044214100
2.83-2.980.22072100.180239714181100
2.98-3.170.22012090.173139864195100
3.17-3.420.19462110.161340034214100
3.42-3.760.20252110.155739994210100
3.76-4.30.15872100.13440084218100
4.3-5.420.13732110.128240124223100
5.42-44.820.16762150.15114091430699
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)
11.20350.2381.11220.50010.24622.7369-0.12780.14510.1174-0.06270.13-0.0219-0.54120.19530.02430.3306-0.02520.03960.18140.03170.2343-24.074620.5837-27.0973
21.46290.15320.73341.0690.36542.97380.02270.0194-0.1390.01230.0948-0.02840.0470.0537-0.14790.20520.01090.02770.16450.01120.2522-21.52058.2362-18.6741
31.78060.39490.4741.18130.74463.7121-0.1255-0.2308-0.24720.10940.15280.08150.1399-0.0021-0.07340.2090.01650.01970.17270.03740.2231-18.404313.3582-7.2975
42.2490.18540.44831.88460.69643.6967-0.025-0.42030.19720.10670.06140.1137-0.5924-0.3065-0.07070.36150.0550.06440.3189-0.00710.2164-22.562423.5094-2.2449
52.3402-0.0055-0.20051.96160.20871.8176-0.1344-0.16940.3718-0.28630.12430.1291-1.064-0.00920.08050.63380.02740.00490.237-0.03470.2847-19.977831.8943-8.6492
61.55090.00810.41.21270.28432.3537-0.2248-0.03120.3034-0.27250.0888-0.0171-0.88680.07770.0940.54830.00550.02190.21810.00560.2679-19.77929.9262-17.479
71.9167-0.2802-0.62671.73890.29931.4481-0.04470.20360.202-0.05020.06910.36580.1177-0.57190.01450.1874-0.05060.00320.38760.0770.3227-52.696518.3894-44.4039
81.50590.0439-0.25321.2718-0.27722.83440.01860.12950.2147-0.01230.11310.3358-0.3239-0.6719-0.13530.17530.0532-0.0180.33180.05950.2769-49.653328.595-48.3265
91.698-0.4837-0.70862.0952-0.11423.01120.09780.06630.2694-0.13130.0410.0742-0.3569-0.247-0.12810.22540.01010.00930.20810.04630.2804-40.151731.3699-52.203
102.8398-0.5154-0.36632.45-0.01953.20910.12210.3979-0.1047-0.4628-0.0608-0.16420.2968-0.1906-0.07250.2731-0.01670.01770.25950.02240.1809-34.209615.7765-61.3364
112.489-0.173-0.43831.666-0.12362.4037-0.12130.0795-0.3717-0.2710.07650.08650.5681-0.27480.02640.2944-0.0854-0.01140.20130.02220.2568-40.17457.8915-53.0919
121.5634-0.7297-0.34251.68340.13722.668-0.17760.0309-0.23510.03630.09820.12780.5264-0.29570.04290.3611-0.05280.02920.21430.03140.277-39.54737.511-46.8872
131.59960.215-0.63652.36640.22932.9362-0.05940.2045-0.0951-0.3414-0.0311-0.08030.08220.03380.07640.20390.030.03660.2086-0.00240.20231.92720.5388-64.3819
142.14730.6256-1.04811.8171-0.04723.1966-0.12330.1836-0.3069-0.1875-0.0305-0.09010.26760.04540.1450.24430.04640.03850.2252-0.01840.26151.086613.8195-61.3885
151.60790.2187-0.47871.77370.10832.4586-0.06240.1284-0.2886-0.1632-0.0692-0.18560.42460.21590.1620.30560.06840.06940.2172-0.00830.31594.04679.5147-56.7635
164.976-0.8769-1.352.96150.0863.8629-0.5456-0.0397-0.58530.32360.1042-0.12450.83050.13480.38740.37430.01820.04780.19060.01770.3236-1.18285.7954-48.215
171.62950.1182-0.851.3660.42842.8821-0.2197-0.3492-0.41170.24970.0019-0.04440.57570.31720.18460.26150.05940.01870.25310.05920.24641.213412.787-42.8709
181.5723-0.78590.11122.8478-0.95332.29640.016-0.1910.14310.1472-0.02220.0392-0.22020.04280.01430.2022-0.01940.00960.2312-0.03790.2176-2.756531.6091-43.3151
192.65490.4809-0.36491.9311.52123.64260.08590.3290.216-0.3589-0.10690.0745-0.4986-0.11850.01960.22770.01630.01420.21970.0150.2397-0.291633.2034-58.5941
201.1812-0.0361-0.59493.1714-0.90241.5988-0.0174-0.33790.07730.1382-0.1294-0.6795-0.10880.43590.16760.27-0.05440.01820.35140.00210.372711.3432.8327-47.1117
214.2702-1.1732-0.04263.28830.59662.5815-0.2012-0.4196-0.34510.52980.18640.27330.4587-0.4641-0.04830.3643-0.03210.09660.33690.01440.27678.839621.1699-10.5599
224.3368-1.0207-0.25353.33940.95983.8764-0.2644-0.39920.76550.50040.4761-0.0658-0.3086-0.2696-0.06590.37020.02110.02150.3342-0.07740.472313.618931.8804-11.8279
234.628-1.18560.80273.63220.88964.1448-0.0387-0.31080.65860.32320.2768-0.0933-0.6965-0.2541-0.1920.41950.00960.02710.2829-0.10610.454114.783932.1876-12.8345
242.9605-0.22930.94753.13210.71981.7497-0.0692-0.32970.91360.25810.3698-0.6587-0.63820.3361-0.11790.4295-0.0598-0.03240.3613-0.16660.61824.629533.8815-12.2091
251.22461.17861.46392.98421.22121.80540.07620.23210.56060.00710.3286-1.0396-0.23790.8935-0.39540.33-0.0681-0.06620.6236-0.22430.856635.354530.154-16.1286
262.8881-1.2522-0.3094.23920.98363.80170.07910.2737-0.43950.25160.0798-0.18580.63940.2084-0.14280.34270.0294-0.03860.2591-0.07270.413223.841411.2454-20.0534
277.06013.0985-1.36295.03640.55361.4765-0.0232-1.4325-0.08011.4396-0.0762-0.39670.78490.62320.12650.82530.1101-0.15290.52860.00310.54827.00529.2432-6.8381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 40 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 41 THROUGH 157 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 158 THROUGH 180 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 181 THROUGH 237 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 238 THROUGH 268 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 269 THROUGH 318 )A0
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 1 THROUGH 40 )B0
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 41 THROUGH 106 )B0
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 107 THROUGH 176 )B0
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 177 THROUGH 237 )B0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 238 THROUGH 285 )B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 286 THROUGH 321 )B0
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 1 THROUGH 64 )C0
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 65 THROUGH 106 )C0
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 107 THROUGH 137 )C0
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 138 THROUGH 158 )C0
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 159 THROUGH 193 )C0
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 194 THROUGH 268 )C0
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 269 THROUGH 297 )C0
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 298 THROUGH 318 )C0
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 2 THROUGH 40 )D0
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 41 THROUGH 64 )D0
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 65 THROUGH 106 )D0
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 107 THROUGH 176 )D0
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 177 THROUGH 199 )D0
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 200 THROUGH 297 )D0
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 298 THROUGH 318 )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://pdbjlvh1.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