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- PDB-4s13: Ferulic Acid Decarboxylase (FDC1) -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4s13
TitleFerulic Acid Decarboxylase (FDC1)
ComponentsFerulic acid decarboxylase 1
KeywordsLYASE / Decarboxylase
Function / homology
Function and homology information


ferulate catabolic process / phenacrylate decarboxylase / ferulate metabolic process / cinnamic acid catabolic process / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ubiquinone biosynthetic process / carboxy-lyase activity / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4570 / UbiD-like decarboxylase/ferulic acid decarboxylase 1 / : / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4570 / UbiD-like decarboxylase/ferulic acid decarboxylase 1 / : / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
4-ethenylphenol / Ferulic acid decarboxylase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.348 Å
AuthorsLee, S.G. / Bhuiya, M.W. / Yu, O. / Jez, J.M.
CitationJournal: Appl.Environ.Microbiol. / Year: 2015
Title: Structure and Mechanism of Ferulic Acid Decarboxylase (FDC1) from Saccharomyces cerevisiae.
Authors: Bhuiya, M.W. / Lee, S.G. / Jez, J.M. / Yu, O.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferulic acid decarboxylase 1
B: Ferulic acid decarboxylase 1
C: Ferulic acid decarboxylase 1
D: Ferulic acid decarboxylase 1
E: Ferulic acid decarboxylase 1
F: Ferulic acid decarboxylase 1
G: Ferulic acid decarboxylase 1
H: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,45413
Polymers449,8538
Non-polymers6015
Water21,4201189
1
A: Ferulic acid decarboxylase 1
C: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7044
Polymers112,4632
Non-polymers2402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-46 kcal/mol
Surface area35500 Å2
MethodPISA
2
B: Ferulic acid decarboxylase 1
E: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5843
Polymers112,4632
Non-polymers1201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-47 kcal/mol
Surface area35510 Å2
MethodPISA
3
D: Ferulic acid decarboxylase 1
F: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5843
Polymers112,4632
Non-polymers1201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-45 kcal/mol
Surface area36130 Å2
MethodPISA
4
G: Ferulic acid decarboxylase 1
H: Ferulic acid decarboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5843
Polymers112,4632
Non-polymers1201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-48 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)251.963, 120.995, 159.560
Angle α, β, γ (deg.)90.00, 121.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ferulic acid decarboxylase 1


Mass: 56231.676 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: FDC1, YDR539W, D3703.2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q03034, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-4VP / 4-ethenylphenol


Mass: 120.149 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1189 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5; 10% PEG 6000; and 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.348→50 Å / Num. obs: 162530 / % possible obs: 96.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.35-2.393.20.492169.3
2.39-2.433.20.454179.2
2.43-2.483.20.387193.7
2.48-2.533.40.358197.2
2.53-2.593.70.327197.5
2.59-2.653.90.301198.4
2.65-2.713.90.263198.6
2.71-2.793.90.231198.6
2.79-2.873.90.214198.7
2.87-2.963.90.191198.8
2.96-3.073.90.166198.8
3.07-3.193.80.144198.9
3.19-3.333.80.128198.9
3.33-3.513.80.113199.1
3.51-3.733.70.099199.1
3.73-4.023.70.089199.2
4.02-4.423.70.079199.2
4.42-5.063.70.074199.2
5.06-6.373.70.073199.4
6.37-503.70.055199

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.348→47.049 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 8142 5.02 %
Rwork0.1705 --
obs0.1727 162293 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.66 Å2
Refinement stepCycle: LAST / Resolution: 2.348→47.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30440 0 45 1189 31674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831262
X-RAY DIFFRACTIONf_angle_d1.11242449
X-RAY DIFFRACTIONf_dihedral_angle_d15.33411594
X-RAY DIFFRACTIONf_chiral_restr0.0474785
X-RAY DIFFRACTIONf_plane_restr0.0065401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.348-2.37470.2692020.22573527X-RAY DIFFRACTION66
2.3747-2.40260.30651920.23573930X-RAY DIFFRACTION74
2.4026-2.43190.30152240.23494247X-RAY DIFFRACTION80
2.4319-2.46270.28922550.22654911X-RAY DIFFRACTION91
2.4627-2.49510.2872740.21955216X-RAY DIFFRACTION97
2.4951-2.52930.27142730.21285207X-RAY DIFFRACTION97
2.5293-2.56540.26942800.2175178X-RAY DIFFRACTION97
2.5654-2.60370.27112870.21225197X-RAY DIFFRACTION98
2.6037-2.64440.2612820.21055263X-RAY DIFFRACTION98
2.6444-2.68770.27222790.20525314X-RAY DIFFRACTION99
2.6877-2.73410.24983000.19225204X-RAY DIFFRACTION99
2.7341-2.78380.2383020.19495228X-RAY DIFFRACTION99
2.7838-2.83730.26732940.19975279X-RAY DIFFRACTION99
2.8373-2.89520.27282890.19745286X-RAY DIFFRACTION99
2.8952-2.95820.26942870.19495273X-RAY DIFFRACTION99
2.9582-3.0270.25582790.19295313X-RAY DIFFRACTION99
3.027-3.10270.26042380.25294X-RAY DIFFRACTION99
3.1027-3.18650.24112900.18655303X-RAY DIFFRACTION99
3.1865-3.28030.21322610.1875292X-RAY DIFFRACTION99
3.2803-3.38610.22422860.18365321X-RAY DIFFRACTION99
3.3861-3.50710.21782760.16745307X-RAY DIFFRACTION99
3.5071-3.64750.19262620.16285314X-RAY DIFFRACTION99
3.6475-3.81340.20042900.15595318X-RAY DIFFRACTION99
3.8134-4.01440.17052900.14415328X-RAY DIFFRACTION99
4.0144-4.26570.15572590.12925364X-RAY DIFFRACTION99
4.2657-4.59480.16962820.12435299X-RAY DIFFRACTION99
4.5948-5.05670.16682670.1275368X-RAY DIFFRACTION99
5.0567-5.78730.17332590.14975412X-RAY DIFFRACTION99
5.7873-7.2870.20133060.16315372X-RAY DIFFRACTION99
7.287-47.05820.1882770.16745286X-RAY DIFFRACTION96
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)
11.2504-0.67590.09552.36520.30571.9538-0.0327-0.1457-0.1160.20930.0611-0.26050.14840.021-0.03940.2884-0.0379-0.0070.18760.02140.3336202.6512-126.5399119.665
21.4099-0.18130.4181.9548-0.55072.1619-0.0674-0.08480.26480.33790.0065-0.7584-0.25880.44460.02670.4183-0.0448-0.10720.34-0.01610.6395215.359-119.8814121.001
31.3319-0.6514-0.06421.514-0.20840.9936-0.0441-0.18870.0940.0584-0.0114-0.0992-0.28790.03980.04870.4322-0.0263-0.00720.2738-0.01780.2528195.7959-100.4504109.4518
43.13280.72531.36830.91640.14931.40570.0584-0.4267-0.08050.1626-0.00970.06530.0085-0.5475-0.05690.5221-0.0293-0.02140.43780.00120.2597175.8762-103.261105.6187
51.5215-0.82670.17551.4777-0.29532.26920.0383-0.0638-0.104-0.0133-0.0108-0.07590.32970.2005-0.03120.3719-0.00220.01150.24990.02740.2998202.4837-65.1331120.623
65.67172.5724.19173.82520.80985.2461-0.0596-0.45510.91040.1146-0.5732-0.3855-0.72490.30390.57580.4279-0.0541-0.01710.52860.01860.5403217.2572-53.6261123.3824
71.6683-0.4220.42030.992-0.82373.73510.0348-0.17310.25580.0089-0.0768-0.279-0.15980.61390.02590.3716-0.03010.0160.4036-0.02020.3995212.8549-56.954123.9626
81.6488-0.42490.01961.3687-0.19630.8977-0.0437-0.0970.1357-0.04520.0296-0.13-0.15130.0830.01020.3214-0.05010.01740.25910.00440.2745193.1758-38.5757110.1192
92.72812.97741.35368.59871.28692.76250.2613-0.4817-0.28960.5125-0.042-0.10280.2303-0.3191-0.23040.2928-0.0016-0.03210.36710.0780.2934166.4246-50.9977105.3459
102.2889-0.5490.52541.32550.26551.17010.19020.1536-0.2685-0.0412-0.08270.09450.1646-0.1905-0.07390.3817-0.0152-0.03870.375-0.04370.2918164.1197-111.011583.571
111.5649-0.11330.35660.65660.57021.01720.19130.29510.32610.0012-0.3141-0.1039-0.63550.34810.0190.57810.0129-00.64490.07780.3598167.2264-91.331673.3324
123.5703-0.7189-0.12971.193-0.05071.560.14080.3717-0.0487-0.1086-0.0648-0.0427-0.3890.2103-0.04160.48080.0358-0.06460.5716-0.0650.2771166.8112-107.900470.6599
132.7085-0.37120.66420.3484-0.04580.82230.05190.13350.13340.0206-0.0364-0.0166-0.0702-0.17670.04770.46540.0042-0.05150.4011-0.03760.3089168.2794-100.458484.622
143.2444-0.8286-0.38121.63850.43271.41930.01240.39260.1931-0.3713-0.0776-0.1818-0.3559-0.03360.03710.5211-0.0392-0.00360.30390.01160.2439194.4011-101.817287.469
153.34682.711-1.26846.3086-2.80784.2137-0.32570.4785-0.4012-0.73290.236-0.46610.3728-0.2860.12870.387-0.01420.04320.2776-0.06420.3317201.3332-129.112197.9051
161.4460.70820.31071.22670.02391.30590.04580.2352-0.2533-0.20840.0497-0.07090.17880.1856-0.10090.33290.091-0.04540.2997-0.10280.3419200.9091-95.3495149.8589
171.36830.07150.42490.64970.50873.90380.03410.26330.0855-0.1029-0.00160.2232-0.3868-0.4544-0.04070.3680.0779-0.08270.356-0.03430.4248183.2318-90.4578148.0788
181.1657-0.06060.050.94010.281.2024-0.04230.15950.1266-0.09570.0509-0.0054-0.15440.07-0.00990.28810.01290.00440.2196-0.01690.2267208.0692-71.2136162.2297
192.1333-0.44370.34110.99540.12611.69090.20070.243-0.2843-0.1565-0.059-0.05360.1856-0.133-0.10280.3464-0.0333-0.04210.2793-0.03030.3179165.64-56.744584.2621
202.1943-0.3975-0.03851.63180.15523.5130.02550.39340.1763-0.2523-0.0324-0.1957-0.39380.1306-0.04040.39310.01690.00450.39730.00760.2643165.0175-42.718872.8685
211.60710.14370.6324-0.2516-0.36830.79550.0670.2847-0.0092-0.1414-0.0233-0.0033-0.0077-0.0335-0.04860.41770.0124-0.01170.3079-0.02150.3029173.2272-44.248584.5399
222.2672-0.9445-0.00321.60220.35531.30110.08140.3570.3219-0.3214-0.1467-0.2379-0.12550.18210.0370.4288-0.05050.06110.34020.06040.2815194.081-38.875388.9969
231.57970.5206-0.19162.8246-1.20792.562-0.01540.2395-0.1933-0.64850.1161-0.25920.70480.13160.01610.58740.06730.03420.3917-0.0430.3371203.2104-66.840598.8608
241.370.1999-0.64391.9532-0.07431.6386-0.0398-0.3838-0.11660.28670.1229-0.45240.3890.73270.15110.43480.1723-0.12890.63-0.08720.4394232.8566-85.8053185.7635
250.34210.35810.30461.49230.41952.23360.103-0.41540.14960.5350.081-0.1874-0.14390.4708-0.00590.54320.0305-0.0710.7576-0.15140.4855232.9956-69.7758193.636
261.4280.43940.62091.32510.3231.30150.0572-0.2086-0.01740.2372-0.00890.02940.03670.0136-0.00970.32680.0612-0.01050.268-0.01530.2457205.3521-78.4693181.7179
272.3215-0.27490.3191.7833-0.4363.78970.0041-0.0428-0.384-0.08160.12740.34990.5549-0.5694-0.1530.4605-0.1424-0.00660.33910.02770.4154225.5899-89.10191.3389
283.1023-0.56880.48842.1684-0.14564.24880.13770.4112-0.0712-0.24230.11890.25570.066-0.2631-0.27740.4406-0.11770.00660.30870.03630.3693229.1577-82.838280.7208
292.9549-0.67660.93552.84120.28255.08360.01860.62010.3655-0.57170.17080.2182-0.6707-0.1717-0.21650.5862-0.0908-0.0310.48680.12070.4271225.3797-74.368174.9585
302.7980.12771.37141.5661-0.98963.4136-0.06910.36660.33190.04490.07830.2167-0.5716-0.2624-0.04260.5176-0.03240.00380.36720.04220.3748229.6128-72.587985.6666
311.68690.47310.64991.3476-0.53763.3281-0.24570.75530.3522-0.0861-0.4965-0.4015-0.71831.12010.31220.617-0.2837-0.0830.77630.29570.4567255.8908-70.359388.4203
322.458-0.4344-0.69043.0799-1.79553.4580.26081.6584-0.3031-0.52420.0077-0.13540.18780.5580.07320.58670.1477-0.05551.1191-0.09040.3763265.781-97.286897.9643
333.2703-1.33811.36310.9925-0.48562.07320.09610.2302-0.2969-0.0081-0.05360.1007-0.01930.1573-0.02810.308-0.02350.04270.24240.00620.2941264.5847-95.744121.0733
344.3899-0.24610.32031.2286-0.53742.96660.0050.65590.70080.0646-0.0003-0.267-0.66580.55140.04660.4565-0.09130.01180.51850.0830.4231279.1862-86.8759120.1822
351.7384-0.97592.29821.3509-1.55043.2881-0.5830.34170.45940.4775-0.1321-0.2454-1.06430.38630.20550.7772-0.185-0.12260.27330.06590.3965252.579-72.3632109.938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 161 )
2X-RAY DIFFRACTION2chain 'A' and (resid 162 through 316 )
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 453 )
4X-RAY DIFFRACTION4chain 'A' and (resid 454 through 503 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 153 )
6X-RAY DIFFRACTION6chain 'B' and (resid 154 through 209 )
7X-RAY DIFFRACTION7chain 'B' and (resid 210 through 316 )
8X-RAY DIFFRACTION8chain 'B' and (resid 317 through 470 )
9X-RAY DIFFRACTION9chain 'B' and (resid 471 through 503 )
10X-RAY DIFFRACTION10chain 'C' and (resid 3 through 186 )
11X-RAY DIFFRACTION11chain 'C' and (resid 187 through 216 )
12X-RAY DIFFRACTION12chain 'C' and (resid 217 through 265 )
13X-RAY DIFFRACTION13chain 'C' and (resid 266 through 345 )
14X-RAY DIFFRACTION14chain 'C' and (resid 346 through 470 )
15X-RAY DIFFRACTION15chain 'C' and (resid 471 through 503 )
16X-RAY DIFFRACTION16chain 'D' and (resid 3 through 118 )
17X-RAY DIFFRACTION17chain 'D' and (resid 119 through 316 )
18X-RAY DIFFRACTION18chain 'D' and (resid 317 through 503 )
19X-RAY DIFFRACTION19chain 'E' and (resid 3 through 153 )
20X-RAY DIFFRACTION20chain 'E' and (resid 154 through 265 )
21X-RAY DIFFRACTION21chain 'E' and (resid 266 through 368 )
22X-RAY DIFFRACTION22chain 'E' and (resid 369 through 470 )
23X-RAY DIFFRACTION23chain 'E' and (resid 471 through 503 )
24X-RAY DIFFRACTION24chain 'F' and (resid 3 through 148 )
25X-RAY DIFFRACTION25chain 'F' and (resid 149 through 308 )
26X-RAY DIFFRACTION26chain 'F' and (resid 309 through 503 )
27X-RAY DIFFRACTION27chain 'G' and (resid 4 through 75 )
28X-RAY DIFFRACTION28chain 'G' and (resid 76 through 153 )
29X-RAY DIFFRACTION29chain 'G' and (resid 154 through 265 )
30X-RAY DIFFRACTION30chain 'G' and (resid 266 through 344 )
31X-RAY DIFFRACTION31chain 'G' and (resid 345 through 470 )
32X-RAY DIFFRACTION32chain 'G' and (resid 471 through 503 )
33X-RAY DIFFRACTION33chain 'H' and (resid 4 through 133 )
34X-RAY DIFFRACTION34chain 'H' and (resid 134 through 308 )
35X-RAY DIFFRACTION35chain 'H' and (resid 309 through 503 )

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