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- PDB-6thc: Crystal structure of Mycobacterium smegmatis CoaB in complex with... -

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Basic information

Entry
Database: PDB / ID: 6thc
TitleCrystal structure of Mycobacterium smegmatis CoaB in complex with CTP and (4-hydroxyphenyl)(2,3,4-trihydroxyphenyl)methanone
ComponentsCoenzyme A biosynthesis bifunctional protein CoaBC
KeywordsLIGASE / CoaBC / bifunctional Phosphopantothenoylcysteine decarboxylase/phosphopantothenate-cysteine ligase / phosphopantothenate-cysteine ligase / Phosphopantothenoylcysteine decarboxylase / phosphopantothenoylcysteine synthetase
Function / homology
Function and homology information


pantothenate catabolic process / phosphopantothenoylcysteine decarboxylase / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / phosphopantothenoylcysteine decarboxylase activity / coenzyme A biosynthetic process / FMN binding / metal ion binding
Similarity search - Function
Coenzyme A biosynthesis bifunctional protein CoaBC / DNA/pantothenate metabolism flavoprotein, C-terminal / CoaB-like superfamily / DNA / pantothenate metabolism flavoprotein / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein
Similarity search - Domain/homology
ACETATE ION / CYTIDINE-5'-TRIPHOSPHATE / Chem-N9N / Coenzyme A biosynthesis bifunctional protein CoaBC
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.033 Å
AuthorsMendes, V. / Blaszczyk, M. / Bryant, O. / Cory-Wright, J. / Blundell, T.L.
Funding support1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation
CitationJournal: Nat Commun / Year: 2021
Title: Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site.
Authors: Mendes, V. / Green, S.R. / Evans, J.C. / Hess, J. / Blaszczyk, M. / Spry, C. / Bryant, O. / Cory-Wright, J. / Chan, D.S. / Torres, P.H.M. / Wang, Z. / Nahiyaan, N. / O'Neill, S. / Damerow, S. ...Authors: Mendes, V. / Green, S.R. / Evans, J.C. / Hess, J. / Blaszczyk, M. / Spry, C. / Bryant, O. / Cory-Wright, J. / Chan, D.S. / Torres, P.H.M. / Wang, Z. / Nahiyaan, N. / O'Neill, S. / Damerow, S. / Post, J. / Bayliss, T. / Lynch, S.L. / Coyne, A.G. / Ray, P.C. / Abell, C. / Rhee, K.Y. / Boshoff, H.I.M. / Barry, C.E. / Mizrahi, V. / Wyatt, P.G. / Blundell, T.L.
History
DepositionNov 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: 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 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
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: Coenzyme A biosynthesis bifunctional protein CoaBC
B: Coenzyme A biosynthesis bifunctional protein CoaBC
C: Coenzyme A biosynthesis bifunctional protein CoaBC
D: Coenzyme A biosynthesis bifunctional protein CoaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,84321
Polymers99,0964
Non-polymers3,74717
Water5,260292
1
A: Coenzyme A biosynthesis bifunctional protein CoaBC
B: Coenzyme A biosynthesis bifunctional protein CoaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,39210
Polymers49,5482
Non-polymers1,8448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-28 kcal/mol
Surface area19220 Å2
MethodPISA
2
C: Coenzyme A biosynthesis bifunctional protein CoaBC
D: Coenzyme A biosynthesis bifunctional protein CoaBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,45111
Polymers49,5482
Non-polymers1,9039
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-29 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.010, 77.371, 144.351
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Coenzyme A biosynthesis bifunctional protein CoaBC / DNA/pantothenate metabolism flavoprotein


Mass: 24773.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: coaBC, MSMEG_3054 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0QWT2, phosphopantothenoylcysteine decarboxylase, phosphopantothenate-cysteine ligase (CTP)

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Non-polymers , 5 types, 309 molecules

#2: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-N9N / (4-hydroxyphenyl)-[2,3,4-tris(oxidanyl)phenyl]methanone


Mass: 246.215 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H10O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% w/v PEG 8000 0.1M MES pH 6.0 0.2M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.03→77.37 Å / Num. obs: 55496 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 35.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Net I/σ(I): 13.1 / Num. measured all: 360758 / Scaling rejects: 488
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.03-2.146.70.8465343779590.7380.3540.9192.4100
6.43-77.375.70.0461100019280.9980.020.0531.999.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.8 Å72.18 Å
Translation5.8 Å72.18 Å

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
Aimless0.5.15data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QJI
Resolution: 2.033→72.176 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.88
RfactorNum. reflection% reflection
Rfree0.2407 2792 5.04 %
Rwork0.1841 --
obs0.187 55419 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.75 Å2 / Biso mean: 48.9335 Å2 / Biso min: 18.8 Å2
Refinement stepCycle: final / Resolution: 2.033→72.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 240 292 6752
Biso mean--55.07 46.36 -
Num. residues----874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076536
X-RAY DIFFRACTIONf_angle_d0.9778893
X-RAY DIFFRACTIONf_chiral_restr0.0621046
X-RAY DIFFRACTIONf_plane_restr0.0051155
X-RAY DIFFRACTIONf_dihedral_angle_d19.6593851
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0333-2.06840.32291160.27072579100
2.0684-2.1060.32231360.26062615100
2.106-2.14650.31091420.24122583100
2.1465-2.19030.28431190.23162610100
2.1903-2.23790.27141350.21812607100
2.2379-2.290.25731160.20822630100
2.29-2.34730.26491410.2042609100
2.3473-2.41070.25491520.20532605100
2.4107-2.48170.25711550.20712568100
2.4817-2.56180.30271530.20332582100
2.5618-2.65330.27731550.20582642100
2.6533-2.75960.28471360.20022608100
2.7596-2.88520.25881600.19992593100
2.8852-3.03730.26961280.19592657100
3.0373-3.22760.23041390.18922644100
3.2276-3.47680.22731360.17482651100
3.4768-3.82670.19511320.1532665100
3.8267-4.38030.18521340.15042670100
4.3803-5.51850.20621290.15462719100
5.5185-72.1760.25091780.1857279099
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)
12.8842-0.09392.01242.0791-0.12413.64980.2849-0.3871-0.1793-0.0014-0.1696-0.06710.72140.0132-0.05940.48120-0.05150.14-0.00670.209674.742722.364630.663
25.09113.5627-0.31496.7088-2.52253.86740.53960.3623-1.01370.1915-0.0117-0.27861.44590.0418-0.32010.8259-0.0025-0.16050.2438-0.00220.366368.820215.115631.493
33.39091.47334.28083.95260.97325.7772-0.11461.10110.2059-0.76390.2550.22220.11170.545-0.18590.4580.0092-0.06720.4284-0.03240.198969.313625.499320.5403
41.97580.79040.18131.82910.00042.19030.19460.28460.24620.1646-0.1882-0.3036-0.03750.33340.09220.39560.0218-0.07420.25930.08680.276582.863631.234926.4532
57.0007-0.46971.2781-0.01490.10961.4024-0.03510.36990.74090.0876-0.1883-0.0641-0.07830.23990.13440.38330.0245-0.07660.21810.02260.295868.279335.783825.4723
61.9090.68121.6071.99451.24364.33870.08190.05930.17410.15750.00190.03980.00970.3241-0.00240.32420.04670.00650.2909-0.02730.2263.494835.846836.8557
73.41742.8217-0.00733.70842.567.33850.35540.276-0.37590.17150.1798-0.33660.26490.1708-0.1620.40690.0075-0.01370.3301-0.0460.295262.367130.743142.3243
84.3611-1.1758-0.87871.9535-0.25026.0828-0.0613-0.7874-0.53260.79010.6550.292-0.0103-0.2877-0.4280.45540.0294-0.04230.4102-0.00940.472658.8127.849546.1771
92.8619-5.18961.37579.7943-2.88356.9073-0.6656-0.6399-0.61021.35740.49610.4378-0.2866-0.7170.03680.635-0.14160.07490.46950.06310.454856.806820.990639.9065
106.10931.96671.876.6533-2.27492.18460.06670.206-0.82610.1785-0.1284-0.84370.43470.2891-0.05080.43850.015-0.1150.3415-0.02740.4811106.74855.243544.5207
115.2112-3.0460.52975.84111.15852.8790.00970.25850.09810.0956-0.30580.1512-0.2015-0.30420.19040.2706-0.0379-0.06720.35380.05480.265488.866326.543136.6856
123.0375-0.43850.72964.91880.4251.6324-0.0681-0.18210.01280.31520.056-0.07090.0592-0.24140.01340.262-0.031-0.05630.2812-0.00120.180899.428613.755843.4751
138.3258-3.94630.35654.70690.21882.2308-0.3036-0.05621.753-0.11950.0515-0.4734-0.4686-0.07420.30380.451-0.0494-0.08520.30880.03220.532296.086334.49837.9669
144.11760.43962.10095.84872.67648.8925-0.33160.91980.4496-1.02430.6323-0.3759-0.82421.0055-0.12460.4062-0.20150.00630.61760.03880.543112.557618.432433.7683
155.20322.86616.12231.5843.43537.15251.1446-1.3562-0.43810.1933-0.4885-0.05660.7177-0.9247-0.60630.5177-0.084-0.12820.6550.05330.5933101.330711.605826.3265
167.59273.5609-0.08997.10990.34527.39250.05391.281-0.0903-0.62110.5861-0.68760.49060.5615-0.38110.37810.04020.12890.5655-0.11080.443108.95647.037728.9527
173.06690.29340.50197.0083-0.82982.83730.1549-0.2066-0.3227-0.3822-0.00611.0930.5846-0.3874-0.1470.3071-0.0496-0.05720.37850.04940.375172.66780.25665.3715
180.2444-1.08050.12135.3713-0.10992.7142-0.0465-0.11080.12240.19350.065-0.23990.00570.06850.08510.1651-0.0091-0.00480.28430.03830.269482.751127.4334.917
195.66782.71130.21762.18220.61443.8912-0.06750.281-0.3125-0.15950.05110.20470.2808-0.55690.07120.2053-0.0223-0.01040.37270.00750.281871.58266.84072.111
205.11382.36870.87344.90951.33322.3026-0.15840.14960.7702-0.10910.23821.0964-0.031-0.53370.07390.24540.025-0.02910.38250.06740.465571.372216.26796.1656
213.85630.5841-0.06472.097-0.73114.2993-0.055-0.53550.08041.0576-0.04360.1483-0.15030.16710.05210.29540.02310.01330.35680.02720.172381.467811.688615.37
222.27121.65360.29562.80790.10991.9889-0.30270.14760.1329-0.04850.262-0.2944-0.22820.23910.03370.15090.0268-0.03390.34390.06730.257387.96323.21769.0851
230.1125-0.33560.06772.8902-2.42542.0561-0.1411-0.05510.00320.2479-0.1439-0.7746-0.00130.13260.24820.19310.07080.02310.3590.07290.303492.007410.522610.5042
244.91292.0037-3.57364.4122-2.58546.2281-0.04450.0391-0.1468-0.02910.1121-0.161-0.04030.1428-0.05310.2089-0.00940.00940.1834-0.05340.183389.52785.14732.0973
254.8771.9728-4.00044.87-4.5116.09930.00410.3528-0.4982-0.24210.0638-0.31750.32050.37940.12860.21110.00110.03220.34770.00480.18296.17596.2685-4.8214
268.84321.6205-1.82943.31953.00254.0691-0.24290.72230.3701-0.59060.20230.1616-0.0565-0.4767-0.20970.30310.02320.03210.36590.04120.245587.30394.7271-6.647
277.67581.9751-1.10547.07093.27875.0083-0.12720.79990.5989-0.58890.25111.0716-0.1088-0.6080.13740.4193-0.0534-0.0040.4133-0.00940.39385.27810.2231-9.8919
282.8243-2.77343.22883.5514-4.97669.67310.47950.965-0.3338-1.227-0.1125-0.50181.06580.1618-0.5830.4198-0.0182-0.05440.4592-0.11550.539577.8974-1.7714-3.7684
291.104-0.80540.60043.3026-1.78532.4282-0.1161-0.1660.1086-0.02190.22480.1042-0.0835-0.1238-0.070.2185-0.0765-0.02410.24520.05310.310475.59238.58-3.9847
308.6739-0.979-2.10212.95331.37453.1530.04660.2668-0.308-0.1347-0.03260.16920.1647-0.27120.05110.2394-0.0472-0.03360.25470.07060.310366.73140.0439-7.0653
313.2422-2.04510.13625.065-0.82081.8357-0.11290.08980.3367-0.0741-0.0457-0.62680.03760.29190.17630.227-0.07460.020.29160.03960.309786.942638.6891-4.942
323.8045-0.2971-1.09833.1481-1.1226.12670.1648-0.32290.63580.8864-0.1825-0.4532-1.07410.5460.16370.5397-0.114-0.07820.2583-0.01350.517977.882255.14390.6251
331.38223.0491-2.19466.537-4.73793.3779-0.40030.46880.67780.7081.15670.0363-0.2008-0.4383-0.54281.0115-0.019-0.30180.67330.08360.824967.516539.914314.7493
346.66531.40352.24765.55590.31787.10770.3748-0.30791.17180.86890.20120.3717-0.9848-0.2747-0.2410.54220.05620.13040.2529-0.07080.443864.819354.00014.5688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 184 through 215 )A184 - 215
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 255 )A216 - 255
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 269 )A256 - 269
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 303 )A270 - 303
5X-RAY DIFFRACTION5chain 'A' and (resid 304 through 319 )A304 - 319
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 354 )A320 - 354
7X-RAY DIFFRACTION7chain 'A' and (resid 355 through 381 )A355 - 381
8X-RAY DIFFRACTION8chain 'A' and (resid 382 through 393 )A382 - 393
9X-RAY DIFFRACTION9chain 'A' and (resid 394 through 412 )A394 - 412
10X-RAY DIFFRACTION10chain 'B' and (resid 184 through 196 )B184 - 196
11X-RAY DIFFRACTION11chain 'B' and (resid 197 through 215 )B197 - 215
12X-RAY DIFFRACTION12chain 'B' and (resid 216 through 281 )B216 - 281
13X-RAY DIFFRACTION13chain 'B' and (resid 282 through 319 )B282 - 319
14X-RAY DIFFRACTION14chain 'B' and (resid 320 through 354 )B320 - 354
15X-RAY DIFFRACTION15chain 'B' and (resid 355 through 371 )B355 - 371
16X-RAY DIFFRACTION16chain 'B' and (resid 372 through 412 )B372 - 412
17X-RAY DIFFRACTION17chain 'C' and (resid 184 through 196 )C184 - 196
18X-RAY DIFFRACTION18chain 'C' and (resid 197 through 215 )C197 - 215
19X-RAY DIFFRACTION19chain 'C' and (resid 216 through 236 )C216 - 236
20X-RAY DIFFRACTION20chain 'C' and (resid 237 through 255 )C237 - 255
21X-RAY DIFFRACTION21chain 'C' and (resid 256 through 269 )C256 - 269
22X-RAY DIFFRACTION22chain 'C' and (resid 270 through 303 )C270 - 303
23X-RAY DIFFRACTION23chain 'C' and (resid 304 through 319 )C304 - 319
24X-RAY DIFFRACTION24chain 'C' and (resid 320 through 342 )C320 - 342
25X-RAY DIFFRACTION25chain 'C' and (resid 343 through 354 )C343 - 354
26X-RAY DIFFRACTION26chain 'C' and (resid 355 through 381 )C355 - 381
27X-RAY DIFFRACTION27chain 'C' and (resid 382 through 393 )C382 - 393
28X-RAY DIFFRACTION28chain 'C' and (resid 394 through 412 )C394 - 412
29X-RAY DIFFRACTION29chain 'D' and (resid 184 through 215 )D184 - 215
30X-RAY DIFFRACTION30chain 'D' and (resid 216 through 255 )D216 - 255
31X-RAY DIFFRACTION31chain 'D' and (resid 256 through 309 )D256 - 309
32X-RAY DIFFRACTION32chain 'D' and (resid 310 through 361 )D310 - 361
33X-RAY DIFFRACTION33chain 'D' and (resid 362 through 377 )D362 - 377
34X-RAY DIFFRACTION34chain 'D' and (resid 378 through 412 )D378 - 412

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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

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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

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