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- PDB-5d4t: SeMet-labelled HcgC from Methanocaldococcus jannaschii in space g... -

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Basic information

Entry
Database: PDB / ID: 5d4t
TitleSeMet-labelled HcgC from Methanocaldococcus jannaschii in space group P212121
ComponentsUncharacterized protein MJ0489
KeywordsUNKNOWN FUNCTION / Rossmann-like fold
Function / homologyFeGP cofactor biosynthesis protein, methyltransferase HcgC / FeGP cofactor biosynthesis protein, methyltransferase HcgC / Uncharacterized protein MJ0489
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
Funding support Japan, Germany, 2items
OrganizationGrant numberCountry
JST-PRESTO Japan
Max Planck Society Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Identification of HcgC as a SAM-Dependent Pyridinol Methyltransferase in [Fe]-Hydrogenase Cofactor Biosynthesis.
Authors: Fujishiro, T. / Bai, L. / Xu, T. / Xie, X. / Schick, M. / Kahnt, J. / Rother, M. / Hu, X. / Ermler, U. / Shima, S.
History
DepositionAug 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein MJ0489
B: Uncharacterized protein MJ0489
C: Uncharacterized protein MJ0489
D: Uncharacterized protein MJ0489
E: Uncharacterized protein MJ0489
F: Uncharacterized protein MJ0489
G: Uncharacterized protein MJ0489
H: Uncharacterized protein MJ0489


Theoretical massNumber of molelcules
Total (without water)246,7808
Polymers246,7808
Non-polymers00
Water19811
1
A: Uncharacterized protein MJ0489
B: Uncharacterized protein MJ0489


Theoretical massNumber of molelcules
Total (without water)61,6952
Polymers61,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-17 kcal/mol
Surface area21430 Å2
MethodPISA
2
C: Uncharacterized protein MJ0489
D: Uncharacterized protein MJ0489


Theoretical massNumber of molelcules
Total (without water)61,6952
Polymers61,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-17 kcal/mol
Surface area21450 Å2
MethodPISA
3
E: Uncharacterized protein MJ0489
F: Uncharacterized protein MJ0489


Theoretical massNumber of molelcules
Total (without water)61,6952
Polymers61,6952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-17 kcal/mol
Surface area21750 Å2
MethodPISA
4
G: Uncharacterized protein MJ0489
H: Uncharacterized protein MJ0489


Theoretical massNumber of molelcules
Total (without water)61,6952
Polymers61,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-19 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.430, 145.000, 150.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid A
31chain C and segid A
41chain D and segid A
51chain E and segid A
61chain F and segid A
71chain G and segid A
81chain H and segid A

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid AB0
311chain C and segid AC0
411chain D and segid AD0
511chain E and segid AE0
611chain F and segid AF0
711chain G and segid AG0
811chain H and segid AH0

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Components

#1: Protein
Uncharacterized protein MJ0489 / HcgC


Mass: 30847.480 Da / Num. of mol.: 8 / Fragment: Rossmann-like domain, residues 2-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0489 / Plasmid: pET24b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57913
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25 % (w/v) PEP426, 0.1 M Tris-HCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.979
SYNCHROTRONSLS X10SA20.971
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELOct 13, 2014
PSI PILATUS 6M2PIXELOct 13, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1A double-crystal Si(111) monochromatorMADMx-ray1
2A double-crystal Si(111) monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9711
ReflectionResolution: 2.9→50 Å / Num. obs: 132512 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 81.17 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.14 / Χ2: 1.114 / Net I/σ(I): 11.49 / Num. measured all: 978478
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.9-30.721.5951.589788212841128371.711100
3-3.20.890.9422.5515789821035210181.01299.9
3.2-3.50.9660.4734.4116560323257232390.51199.9
3.5-40.990.2378.318670424921249060.25599.9
4-4.70.9980.09416.6714017219395193910.102100
4.7-5.90.9990.07221.0911717815389153870.078100
5.9-80.9990.05824.8267388943794340.063100
8-1210.03339.3632504445344490.03599.9
1210.03244.1313149188518510.03598.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHARPphasing
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.9→48.563 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 3494 5.06 %
Rwork0.2279 65561 -
obs0.2294 69055 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.74 Å2 / Biso mean: 86.3585 Å2 / Biso min: 42.7 Å2
Refinement stepCycle: final / Resolution: 2.9→48.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15758 0 0 11 15769
Biso mean---55.12 -
Num. residues----1954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01516066
X-RAY DIFFRACTIONf_angle_d1.66321733
X-RAY DIFFRACTIONf_chiral_restr0.0712548
X-RAY DIFFRACTIONf_plane_restr0.0092739
X-RAY DIFFRACTIONf_dihedral_angle_d12.8675963
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9350X-RAY DIFFRACTION10.469TORSIONAL
12B9350X-RAY DIFFRACTION10.469TORSIONAL
13C9350X-RAY DIFFRACTION10.469TORSIONAL
14D9350X-RAY DIFFRACTION10.469TORSIONAL
15E9350X-RAY DIFFRACTION10.469TORSIONAL
16F9350X-RAY DIFFRACTION10.469TORSIONAL
17G9350X-RAY DIFFRACTION10.469TORSIONAL
18H9350X-RAY DIFFRACTION10.469TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.93970.38281590.357325702729100
2.9397-2.98170.41091440.354625562700100
2.9817-3.02620.38371280.328426312759100
3.0262-3.07350.33381450.310425892734100
3.0735-3.12390.31661550.302525662721100
3.1239-3.17770.30231360.300226032739100
3.1777-3.23550.34121320.289925902722100
3.2355-3.29770.31351480.30525942742100
3.2977-3.3650.28121460.281126092755100
3.365-3.43820.2861320.279525982730100
3.4382-3.51810.3051210.260426002721100
3.5181-3.60610.26661420.237826092751100
3.6061-3.70350.26561310.230926262757100
3.7035-3.81250.26771540.231125872741100
3.8125-3.93550.24761470.236626042751100
3.9355-4.07610.2811500.22226152765100
4.0761-4.23920.22461470.206226052752100
4.2392-4.4320.22851510.182326192770100
4.432-4.66550.22131110.176426572768100
4.6655-4.95750.20121440.182426422786100
4.9575-5.33990.24931450.193926332778100
5.3399-5.87640.22881330.218126662799100
5.8764-6.72480.23541290.226526922821100
6.7248-8.46530.23771380.211227182856100
8.4653-48.570.25271260.21572782290898
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)
12.3001-1.1286-0.72062.01051.38593.5094-0.08110.32290.2646-1.43170.2792-0.4085-1.14820.341-0.12650.7243-0.1308-0.02810.5728-0.02010.44776.4215128.689563.5572
27.4585-0.5181-0.77384.26662.46654.0736-0.1286-0.04570.6930.07280.1674-0.6953-0.80090.07220.05580.7885-0.1044-0.08120.6723-0.08920.736986.5757141.690281.2982
34.87312.7659-1.0257.36480.72512.5875-0.1224-0.47190.59620.3685-0.36660.9931-0.28340.01260.420.7175-0.0604-0.00530.5974-0.21170.685771.4637134.768885.8429
40.2748-0.23670.38314.88561.64553.2539-0.1275-0.01940.32980.14480.07350.08590.05110.3140.08610.6478-0.02630.08360.7287-0.1210.582875.885120.304465.4742
50.9097-0.0752-0.52538.99175.08245.29680.0519-0.1709-0.06960.86020.1329-0.36980.59940.2144-0.33040.50860.0959-0.09870.5643-0.11240.504378.008290.800367.0392
66.5788-1.5653-3.84175.28470.41982.83230.37550.117-0.3167-0.411-0.2733-0.0630.01050.5974-0.06650.54340.02720.01150.5688-0.07620.473385.417582.415351.312
74.5539-2.68060.54225.7282-1.17660.82950.19710.498-0.2152-0.339-0.41460.41740.3751-0.07560.21430.58320.01380.00160.5883-0.20710.604967.953890.830851.598
82.32510.9721.44775.48851.82172.933-0.00680.1399-0.0934-0.0906-0.1224-0.0838-0.0355-0.12570.06360.50810.0295-0.0150.5154-0.13640.495275.8856105.094771.087
93.9293-0.8954-0.32844.85542.87763.97260.1241-0.91280.98251.1633-0.58240.64440.3399-0.28430.52250.7301-0.06310.27250.9111-0.29080.812743.2102119.696790.7887
105.5764-2.7475-3.50575.9464-0.69575.34210.1917-0.70440.31620.1627-0.45711.1482-0.4464-1.2322-0.0610.8482-0.04350.02171.3365-0.66461.507434.356134.170693.6574
112.38850.0774-1.32872.91292.34568.78250.067-0.27890.94620.29530.11240.5412-0.72130.0394-0.25190.6849-0.07070.05830.8344-0.41081.150949.7021136.735787.3583
122.72251.9421-0.07544.51522.58553.22790.0093-0.2880.65450.41450.1480.03810.09740.0512-0.1190.6155-0.02230.04440.6327-0.20140.560743.6561113.055178.452
131.26110.0896-0.87285.92593.94554.4648-0.26780.46090.0679-0.90350.02720.4238-0.3833-0.01780.17270.65330.051-0.20750.7453-0.09480.66840.4231107.295550.2693
145.17872.53530.83987.1002-0.93171.8197-0.00940.50230.4847-0.0511-0.09220.70490.1086-0.86130.08860.63790.03640.00990.9172-0.22290.6230.433394.133248.7369
159.25211.56652.17053.66862.47745.41190.0558-0.1411-0.42210.1874-0.03320.17750.486-0.1721-0.00470.63610.02940.0840.6952-0.08460.368843.702786.636552.2699
162.5493-0.37460.44875.71972.44833.1397-0.02810.13240.06440.00370.10740.1516-0.0636-0.2111-0.15350.49920.0388-0.06080.5326-0.07180.427744.3493111.641461.0838
171.7335-0.49460.25033.5527-3.35532.47080.14740.60670.4478-1.2565-0.6949-1.15571.11340.29550.2820.95510.27970.25931.03840.10360.821492.1777113.1081-11.2776
181.4933-0.3497-0.81023.7434-0.44050.6184-0.23071.66090.1987-0.8537-0.4174-0.58990.37822.48290.55420.97960.10320.31542.04730.65551.433597.4282130.534-21.2859
193.82642.9594-0.01812.47041.24853.2902-0.39070.2212-1.0539-0.25960.3543-2.2511-1.9578-0.1620.36691.21730.00220.04551.62920.9622.2686102.0805141.8335-18.0017
202.98170.9518-1.82062.181-0.91423.53690.16720.30181.1-0.5216-0.1543-0.562-0.4039-0.02190.13440.71430.12630.1520.87260.28761.157984.8306136.1184-10.4413
211.56121.5348-1.05882.1914-4.72713.755-0.40890.23780.53910.16910.1391-0.11590.1247-0.0672-0.01050.74360.10970.00110.73450.16970.826787.3667113.5255-0.8744
222.46150.46410.43374.2882-0.17671.95880.6223-0.24420.86110.0088-0.8016-0.2010.21350.55780.05350.60520.1510.15430.6867-0.0220.747795.7057112.8361.9565
234.6679-1.59540.3562.05651.01675.87450.3983-0.53321.54591.079-0.2817-0.64250.30951.23970.02060.84780.00880.20821.15570.09680.8115107.6186119.7756-2.0138
241.9842-1.04321.30632.8471-1.7342.8880.3860.62240.0594-0.674-0.3221-0.06110.39190.1421-0.01760.77040.14690.18210.8162-0.01510.618486.5705110.5614-7.8852
253.1984-1.1758-0.15268.863-6.8226.6858-0.32070.07550.33131.3405-0.4937-0.8977-1.2749-0.09630.54410.68640.0607-0.07360.5089-0.1610.690794.0768113.628620.9035
265.4204-4.14431.92267.0669-3.06542.0052-1.2142-0.20050.2481.3131-0.3374-0.0568-0.31010.75550.81750.71740.12010.03520.9421-0.07810.637498.953892.818433.6591
275.1891-0.6426-28.4051-1.62045.9027-0.2748-0.39250.15250.3387-0.3352-0.71550.36670.89940.23180.48790.10780.04580.66790.0870.8247105.397193.677526.3156
283.6505-1.65580.68481.8146-1.75764.08990.04540.4638-0.2865-0.3599-0.3453-0.28340.29930.24130.35290.66360.09590.07530.7659-0.1450.557690.309789.375822.2981
294.8674-6.9914.5252.1863-4.52058.39850.0936-1.2484-0.2956-1.21390.46430.2750.6773-0.5837-0.50590.6451-0.04810.18410.54560.05340.796187.8926112.742811.3576
304.727-0.85683.36256.8025-3.3493.26420.33520.994-0.7579-0.1498-0.2823-0.16780.55010.61310.10030.71930.09680.1420.7882-0.11440.6897101.1706111.42558.3807
311.75880.7898-0.99578.6879-5.83875.03250.1041-0.07410.33960.97430.0926-0.0415-0.64080.008-0.1680.61450.0261-0.0310.6508-0.17830.669588.2376116.317918.1625
320.81310.52881.21735.4991-4.07654.6804-0.1169-0.36920.46160.23630.14020.5873-0.6264-0.1893-0.12960.7120.12590.08680.4876-0.13250.720358.0371133.86747.3713
334.0568-2.13551.75177.2056-4.43568.517-0.1474-0.70410.2674-0.14990.57951.5853-0.6312-0.8939-0.42130.53940.0158-0.02640.61210.05080.987747.5976139.6488-4.4093
345.2982-2.86091.47638.9823-1.70294.6040.03540.7094-0.0187-0.8552-0.2320.51930.0590.13280.19880.5003-0.05530.02120.5476-0.02640.522462.3985136.513-10.4126
351.85-3.31453.22249.4169-9.3552.27190.2166-0.0110.708-1.0126-0.40790.04951.2484-0.11860.23710.69660.0389-0.02390.61-0.00210.571464.9978118.98848.1978
362.6511-0.9361-0.17496.4075-3.27054.62650.23540.5109-0.1896-0.7720.2741.15520.8684-0.9888-0.54570.5468-0.0546-0.02280.6588-0.09440.591751.7637117.02116.8491
371.2128-0.1971-0.76.2686-3.11773.3842-0.1371-0.49380.15890.9132-0.0853-0.3103-0.45950.2560.27640.5596-0.0611-0.01870.4967-0.1080.448365.5063124.599213.2562
381.07650.9164-1.36667.4453-5.35226.2952-0.17110.0872-0.1735-1.6230.13010.05061.7172-0.2683-0.05060.8715-0.0977-0.05140.6466-0.14760.524358.359291.88027.9143
397.86630.1374-1.84414.6953-7.02272.52290.36230.66740.2673-0.2866-0.19450.030.7912-0.4275-0.18460.8516-0.03680.08910.5573-0.12590.533850.866883.093421.6899
408.08147.3454-1.23028.982-0.88781.4180.2604-1.069-0.04530.7802-0.4964-0.32610.07460.07440.23150.68230.068-0.00760.6398-0.00650.5567.002889.320927.0274
410.6635-0.48240.39612.5128-2.75713.0839-0.0153-0.10220.0658-0.4047-0.2769-0.11460.1522-0.15560.37910.7440.01640.00230.4888-0.13760.532563.8273104.42168.2307
421.9243-0.44891.1915.8434-5.22832.4883-0.0520.2405-0.0875-0.69090.04690.09960.63970.0953-0.02690.78740.0186-0.13870.5374-0.22610.52859.3691102.46563.1416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 42 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 116 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 184 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 268 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 66 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 116 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 117 through 184 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 185 through 268 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 13 through 55 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 56 through 106 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 107 through 184 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 185 through 268 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 13 through 55 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 56 through 105 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 106 through 166 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 167 through 268 )D0
17X-RAY DIFFRACTION17chain 'E' and (resid 13 through 41 )E0
18X-RAY DIFFRACTION18chain 'E' and (resid 42 through 92 )E0
19X-RAY DIFFRACTION19chain 'E' and (resid 93 through 116 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 117 through 184 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 185 through 202 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 203 through 221 )E0
23X-RAY DIFFRACTION23chain 'E' and (resid 222 through 233 )E0
24X-RAY DIFFRACTION24chain 'E' and (resid 234 through 268 )E0
25X-RAY DIFFRACTION25chain 'F' and (resid 13 through 41 )F0
26X-RAY DIFFRACTION26chain 'F' and (resid 42 through 55 )F0
27X-RAY DIFFRACTION27chain 'F' and (resid 56 through 105 )F0
28X-RAY DIFFRACTION28chain 'F' and (resid 106 through 184 )F0
29X-RAY DIFFRACTION29chain 'F' and (resid 185 through 202 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 203 through 233 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 234 through 268 )F0
32X-RAY DIFFRACTION32chain 'G' and (resid 13 through 55 )G0
33X-RAY DIFFRACTION33chain 'G' and (resid 56 through 105 )G0
34X-RAY DIFFRACTION34chain 'G' and (resid 106 through 184 )G0
35X-RAY DIFFRACTION35chain 'G' and (resid 185 through 202 )G0
36X-RAY DIFFRACTION36chain 'G' and (resid 203 through 233 )G0
37X-RAY DIFFRACTION37chain 'G' and (resid 234 through 268 )G0
38X-RAY DIFFRACTION38chain 'H' and (resid 13 through 59 )H0
39X-RAY DIFFRACTION39chain 'H' and (resid 60 through 116 )H0
40X-RAY DIFFRACTION40chain 'H' and (resid 117 through 166 )H0
41X-RAY DIFFRACTION41chain 'H' and (resid 167 through 221 )H0
42X-RAY DIFFRACTION42chain 'H' and (resid 222 through 268 )H0

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