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- PDB-5o30: Crystal structure of the novel halohydrin dehalogenase HheG -

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Basic information

Entry
Database: PDB / ID: 5o30
TitleCrystal structure of the novel halohydrin dehalogenase HheG
ComponentsPutative oxidoreductase
KeywordsLYASE / halohydrin dehalogenase / short-chain dehydrogenase/lyase / Rossman-fold
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / ACETATE ION / Putative oxidoreductase / Putative oxidoreductase
Function and homology information
Biological speciesIlumatobacter coccineus YM16-304 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsDiederich, C. / Schallmey, A. / Blankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry of Economic Affairs and Energy (BMWi) within the AiF-ZIM funding scheme Germany
CitationJournal: Acs Catalysis / Year: 2017
Title: HheG, a Halohydrin Dehalogenase with Activity on Cyclic Epoxides
Authors: Koopmeiners, J. / Diederich, C. / Solarczek, J. / Voss, H. / Meyer, J. / Blankenfeldt, W. / Schallemy, A.
History
DepositionMay 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase
E: Putative oxidoreductase
F: Putative oxidoreductase
G: Putative oxidoreductase
H: Putative oxidoreductase
I: Putative oxidoreductase
J: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,36813
Polymers299,15810
Non-polymers2103
Water22,5011249
1
A: Putative oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8737
Polymers119,6634
Non-polymers2103
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-73 kcal/mol
Surface area35280 Å2
MethodPISA
2
E: Putative oxidoreductase
F: Putative oxidoreductase

E: Putative oxidoreductase
F: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)119,6634
Polymers119,6634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area11290 Å2
ΔGint-73 kcal/mol
Surface area35720 Å2
MethodPISA
3
G: Putative oxidoreductase
H: Putative oxidoreductase

G: Putative oxidoreductase
H: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)119,6634
Polymers119,6634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area11290 Å2
ΔGint-75 kcal/mol
Surface area34910 Å2
MethodPISA
4
I: Putative oxidoreductase
J: Putative oxidoreductase

I: Putative oxidoreductase
J: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)119,6634
Polymers119,6634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11300 Å2
ΔGint-74 kcal/mol
Surface area34810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.877, 194.877, 195.179
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11E-375-

HOH

21E-484-

HOH

31F-413-

HOH

41F-483-

HOH

51G-344-

HOH

61I-352-

HOH

71J-338-

HOH

81J-382-

HOH

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Components

#1: Protein
Putative oxidoreductase /


Mass: 29915.795 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ilumatobacter coccineus YM16-304 (bacteria)
Gene: YM304_35350 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: M5A5Y8, UniProt: A0A6C7EF96*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1249 / 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: 3.59 Å3/Da / Density % sol: 65 % / Description: diamond-shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetat pH 4.5, 1M ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.3→87.18 Å / Num. obs: 189092 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rpim(I) all: 0.039 / Net I/σ(I): 21
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 9293 / CC1/2: 0.89 / Rpim(I) all: 0.455 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→65.06 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 21.67
RfactorNum. reflection% reflection
Rfree0.2032 18820 5.11 %
Rwork0.19 --
obs0.1907 188958 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→65.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18881 0 14 1249 20144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319344
X-RAY DIFFRACTIONf_angle_d0.5726254
X-RAY DIFFRACTIONf_dihedral_angle_d9.67811446
X-RAY DIFFRACTIONf_chiral_restr0.0433006
X-RAY DIFFRACTIONf_plane_restr0.0033503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32620.30346020.298811674X-RAY DIFFRACTION100
2.3262-2.35350.28665700.28611720X-RAY DIFFRACTION100
2.3535-2.38220.28645720.289511664X-RAY DIFFRACTION100
2.3822-2.41240.3226770.294411594X-RAY DIFFRACTION100
2.4124-2.44410.31846200.27911652X-RAY DIFFRACTION100
2.4441-2.47760.30875910.279811631X-RAY DIFFRACTION100
2.4776-2.5130.28567140.266811542X-RAY DIFFRACTION100
2.513-2.55050.27556280.257211661X-RAY DIFFRACTION100
2.5505-2.59040.26067080.250511525X-RAY DIFFRACTION100
2.5904-2.63280.24777100.236411635X-RAY DIFFRACTION100
2.6328-2.67820.25686380.248611639X-RAY DIFFRACTION100
2.6782-2.72690.25655740.239611706X-RAY DIFFRACTION100
2.7269-2.77940.24315980.231211618X-RAY DIFFRACTION100
2.7794-2.83610.24017420.226811542X-RAY DIFFRACTION100
2.8361-2.89780.26026200.234511611X-RAY DIFFRACTION100
2.8978-2.96520.24895990.216511857X-RAY DIFFRACTION100
2.9652-3.03940.24365940.218911553X-RAY DIFFRACTION100
3.0394-3.12150.23096360.206811604X-RAY DIFFRACTION100
3.1215-3.21340.21165400.199611754X-RAY DIFFRACTION100
3.2134-3.31710.21786240.20311685X-RAY DIFFRACTION100
3.3171-3.43570.2025980.187111672X-RAY DIFFRACTION100
3.4357-3.57320.21156330.18811668X-RAY DIFFRACTION100
3.5732-3.73580.17256380.163611633X-RAY DIFFRACTION100
3.7358-3.93270.1646620.153611590X-RAY DIFFRACTION100
3.9327-4.17910.14795760.14711695X-RAY DIFFRACTION100
4.1791-4.50170.15356300.143111654X-RAY DIFFRACTION100
4.5017-4.95460.15576760.132711586X-RAY DIFFRACTION100
4.9546-5.67120.16355880.153211717X-RAY DIFFRACTION100
5.6712-7.14360.1916860.174411604X-RAY DIFFRACTION100
7.1436-65.08570.16335760.171611688X-RAY DIFFRACTION100
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)
11.9857-1.2382-1.20681.81241.46273.31670.2277-0.00740.2515-0.4643-0.1161-0.4441-0.56341.023-0.08980.6664-0.24590.0891.2672-0.05430.3433125.852453.32843.1607
20.7669-0.31980.35281.4009-0.68871.4050.05490.13680.0271-0.2511-0.0033-0.1607-0.35980.4382-0.05770.5576-0.04540.03080.7567-0.02370.204108.982552.739542.0369
31.5013-0.64750.04730.29370.22674.201-0.17230.33530.182-0.83280.1794-0.3136-0.69040.5903-0.01810.6188-0.07990.01550.86280.02850.2075112.411955.477350.9966
41.61990.67651.60966.4584-0.39251.7830.1742.30671.0276-1.8748-0.0095-0.6144-1.04760.1386-0.16121.4284-0.35490.13991.12630.0380.6856117.689477.650153.9139
51.2055-0.1703-0.0931.27960.29860.88440.0539-0.00960.0961-0.04990.0435-0.1875-0.5970.5728-0.09760.6038-0.12160.02380.87070.00370.2588114.611356.061458.2601
60.9923-0.8234-0.55052.80141.26824.2782-0.02560.1008-0.14930.36070.2291-0.41790.18841.0772-0.18380.48850.066-0.07631.0975-0.09450.3031123.109646.00881.5932
70.89920.09190.10510.79090.41871.26530.0372-0.1342-0.00620.11550.0148-0.1371-0.31250.3642-0.05850.5493-0.0529-0.02110.73450.0050.1936108.169753.161478.7441
82.21111.53290.50313.70261.42670.87830.1059-0.0058-0.24180.1903-0.024-0.1932-0.13330.534-0.06870.41980.0183-0.01890.71060.0070.2025110.096741.91965.8968
92.4190.7282-1.39080.85570.116.7810.1373-0.26290.27520.0543-0.08270.2043-1.0204-0.4719-0.050.96950.43010.09751.05540.03510.344671.299867.644779.8347
100.64460.04580.06390.740.32191.1820.1031-0.16930.09030.2275-0.01360.1579-0.5522-0.4348-0.09150.6880.10370.02990.81870.02070.222685.237458.741181.1588
112.08260.0468-1.03110.0123-0.22814.21370.3291-0.62150.27820.5937-0.40480.1685-0.9192-0.14530.08140.74820.170.00590.9157-0.01230.235584.183863.147871.9701
124.7243-0.9403-2.17462.25633.97697.07160.5545-2.01322.19531.7836-0.17770.2817-2.84180.2233-0.3741.89020.07070.16540.9273-0.15990.858590.687485.12269.1474
131.42531.0164-0.98951.6322-1.18252.5620.1982-0.14010.22620.2477-0.09230.2296-0.7247-0.4685-0.09810.76380.25230.0220.812-0.00380.249682.402764.800864.553
142.59581.6796-0.84621.3321-1.64948.2127-0.03690.03040.2235-0.16880.12990.1997-0.5971-0.796-0.09310.60220.2814-0.0081.00290.05790.27372.76662.938644.6428
150.8468-0.16540.11260.7043-0.66041.09080.010.08590.0142-0.05820.1440.1876-0.4103-0.5826-0.13890.65840.1609-0.00170.8560.04620.227881.504759.054241.9868
161.096-0.0748-0.17951.61-1.77032.9914-0.030.24530.0153-0.50860.11380.179-0.4814-0.3217-0.09220.57580.16260.01120.82590.01380.216582.27356.815550.9083
171.7337-0.499-0.27774.1474-1.56251.3090.03490.0347-0.2087-0.30340.07620.3703-0.3743-0.5543-0.10770.49380.1127-0.03380.84650.01190.223679.704250.103357.0243
182.27230.73440.13865.6875-0.87073.58090.00590.7003-0.1347-0.8308-0.0098-0.790.20140.34080.01070.3223-0.05020.11350.8676-0.0440.3906119.45933.500936.1695
190.5994-0.18070.27071.4912-0.49590.7864-0.07920.15680.0285-0.1817-0.0108-0.39220.01470.22170.09580.1988-0.01830.04050.6696-0.00950.4008120.91243.676153.5027
201.0222.61780.32577.18320.10171.4191-0.10570.2587-0.0983-0.37030.1945-0.55920.22390.1519-0.08980.2070.01870.02820.685-0.04150.3249107.7893-3.852547.853
214.24420.24750.14395.14750.33823.6884-0.12280.67550.3806-0.5541-0.02960.7194-0.3693-0.48420.15370.2865-0.0166-0.13620.83360.07850.48283.131311.733938.789
221.3513-0.0347-0.06911.07020.11860.4355-0.06550.19130.0401-0.1851-0.00710.2793-0.0532-0.20820.07720.2211-0.0109-0.05030.7304-0.01110.389483.43173.420652.9655
230.37081.44980.70516.33942.05012.0778-0.01980.24180.055-0.132-0.12540.3713-0.2253-0.13420.15750.21960.0218-0.01520.66310.02160.365496.793414.250152.6846
245.82081.63091.56930.64360.74682.9167-0.02440.42590.4229-0.1102-0.36880.5492-0.2321-0.21640.3910.3806-0.0635-0.13271.01380.16251.430553.339524.58858.5928
252.3227-0.33191.1720.0545-0.17090.593-0.08090.34241.1809-0.10720.0374-0.0073-0.30740.0420.05040.4505-0.0231-0.13280.97710.28161.661650.187428.190856.9118
264.7668-1.6332.03360.9692-0.57311.48760.05190.94020.7108-0.2699-0.16010.2927-0.18680.0760.10780.5736-0.1161-0.1881.42550.55521.720659.35525.764547.4544
273.3307-0.3155-0.05271.33160.03720.9215-0.14550.16721.1215-0.07540.01970.0693-0.29680.04120.11720.2777-0.0224-0.06230.85220.04081.113559.654717.138861.0946
283.292-0.05120.03670.8036-0.11040.7628-0.01420.0150.4054-0.00100.0633-0.09510.00110.01390.184-0.0123-0.030.7501-0.02820.810452.73547.625763.7416
296.41050.10771.02911.5739-0.19350.19340.09570.69640.267-0.18450.2938-0.3917-0.1390.2563-0.38260.27440.01830.00030.91450.0561.162347.043413.180158.0168
302.7751-2.89963.00867.3813-0.1555.3142-0.09510.26990.2149-0.91620.1166-1.8439-0.16211.7846-0.02520.6836-0.11970.00861.61880.191.24443.92087.067336.1592
313.2007-0.923-0.10811.03040.19260.8409-0.12020.40170.6939-0.110.12360.1342-0.20060.1266-0.00590.3013-0.0168-0.03840.94260.14711.213539.676815.278456.6071
322.8-0.3620.78790.7114-0.22060.8164-0.0264-0.10621.08050.017-0.04650.0216-0.3055-0.14030.0450.44450.0738-0.06851.02970.00591.839718.014428.505662.1501
332.24-0.1995-0.04360.39250.13690.5616-0.07920.22830.5073-0.0551-0.0310.1141-0.1617-0.16860.09090.23460.0179-0.0450.99390.0391.116517.146711.488261.3794
345.8789-0.23950.86641.5366-0.62250.3535-0.0597-0.51250.75530.1210.08560.4083-0.2977-0.5164-0.03120.29320.0019-0.02520.9899-0.00981.29125.81215.118664.9694
351.94332.41781.02984.1448-1.8128.9635-0.2745-1.44580.49050.75660.25942.2119-1.0974-2.41590.01510.7640.17520.01861.7141-0.47231.618428.852320.334586.3323
362.4094-0.12260.52680.5548-0.10481.0192-0.1001-0.05110.87450.02740.0490.0041-0.2582-0.21780.04170.3030.043-0.00770.9028-0.03641.280233.261317.362965.039
370.41970.3833-0.1560.8487-0.18060.39780.1437-0.2512-0.34710.3083-0.1667-0.39650.17920.07910.03590.9524-0.4479-0.22980.49430.21011.052416.06731.708211.0877
382.37211.7704-0.75343.6218-1.41971.6304-0.13390.0163-0.6423-0.19890.0492-0.74840.7011-0.02450.08180.9082-0.3231-0.20610.44650.12731.14725.597810.93135.088
390.74241.2362-0.432.2133-0.50150.54440.3539-0.4642-0.30140.5667-0.323-0.4940.07910.1633-0.01821.0326-0.4794-0.37790.76770.33031.059238.812927.758519.2687
401.90831.0157-0.06690.82520.18921.82140.5591-0.8305-0.04731.3163-0.4922-0.3259-0.19410.1803-0.06871.5924-0.7926-0.35611.23490.2661.064338.682136.681628.033
411.25291.1034-0.25792.452-0.04750.52220.1402-0.2657-0.29320.3778-0.1947-0.40690.04320.13290.0340.7224-0.3357-0.15860.41970.11920.77131.776337.14657.9061
424.39113.4508-0.83225.4241-1.82830.6660.3622-0.40650.58490.7556-0.1037-0.2232-0.02350.0705-0.24980.8746-0.356-0.29270.51260.15440.822526.577229.832912.5783
438.9832-3.2767-0.66933.63-1.82435.0046-0.4383-0.3831.7355-0.20880.2532-0.8803-1.70631.1370.18581.3855-0.45050.1241.2361-0.07711.042811.460334.981628.6485
440.50630.4255-0.05613.36670.11230.59680.2212-0.3475-0.26340.5608-0.2568-0.13440.13280.0210.02920.9282-0.4166-0.22780.58270.15910.863223.788222.908114.6803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 61)
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 182)
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 207)
4X-RAY DIFFRACTION4chain 'A' and (resid 208 through 222)
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 262)
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 76)
7X-RAY DIFFRACTION7chain 'B' and (resid 77 through 207)
8X-RAY DIFFRACTION8chain 'B' and (resid 208 through 262)
9X-RAY DIFFRACTION9chain 'C' and (resid 6 through 61)
10X-RAY DIFFRACTION10chain 'C' and (resid 62 through 182)
11X-RAY DIFFRACTION11chain 'C' and (resid 183 through 207)
12X-RAY DIFFRACTION12chain 'C' and (resid 208 through 222)
13X-RAY DIFFRACTION13chain 'C' and (resid 223 through 262)
14X-RAY DIFFRACTION14chain 'D' and (resid 6 through 19)
15X-RAY DIFFRACTION15chain 'D' and (resid 20 through 182)
16X-RAY DIFFRACTION16chain 'D' and (resid 183 through 206)
17X-RAY DIFFRACTION17chain 'D' and (resid 207 through 262)
18X-RAY DIFFRACTION18chain 'E' and (resid 6 through 61)
19X-RAY DIFFRACTION19chain 'E' and (resid 62 through 182)
20X-RAY DIFFRACTION20chain 'E' and (resid 183 through 262)
21X-RAY DIFFRACTION21chain 'F' and (resid 5 through 61)
22X-RAY DIFFRACTION22chain 'F' and (resid 62 through 207)
23X-RAY DIFFRACTION23chain 'F' and (resid 208 through 262)
24X-RAY DIFFRACTION24chain 'G' and (resid 6 through 19)
25X-RAY DIFFRACTION25chain 'G' and (resid 20 through 37)
26X-RAY DIFFRACTION26chain 'G' and (resid 38 through 61)
27X-RAY DIFFRACTION27chain 'G' and (resid 62 through 113)
28X-RAY DIFFRACTION28chain 'G' and (resid 114 through 182)
29X-RAY DIFFRACTION29chain 'G' and (resid 183 through 207)
30X-RAY DIFFRACTION30chain 'G' and (resid 208 through 222)
31X-RAY DIFFRACTION31chain 'G' and (resid 223 through 262)
32X-RAY DIFFRACTION32chain 'H' and (resid 6 through 61)
33X-RAY DIFFRACTION33chain 'H' and (resid 62 through 182)
34X-RAY DIFFRACTION34chain 'H' and (resid 183 through 207)
35X-RAY DIFFRACTION35chain 'H' and (resid 208 through 222)
36X-RAY DIFFRACTION36chain 'H' and (resid 223 through 262)
37X-RAY DIFFRACTION37chain 'I' and (resid 6 through 182)
38X-RAY DIFFRACTION38chain 'I' and (resid 183 through 262)
39X-RAY DIFFRACTION39chain 'J' and (resid 6 through 37)
40X-RAY DIFFRACTION40chain 'J' and (resid 38 through 61)
41X-RAY DIFFRACTION41chain 'J' and (resid 62 through 182)
42X-RAY DIFFRACTION42chain 'J' and (resid 183 through 207)
43X-RAY DIFFRACTION43chain 'J' and (resid 208 through 222)
44X-RAY DIFFRACTION44chain 'J' and (resid 223 through 262)

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