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- PDB-3rpf: Protein-protein complex of subunit 1 and 2 of Molybdopterin-conve... -

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Basic information

Entry
Database: PDB / ID: 3rpf
TitleProtein-protein complex of subunit 1 and 2 of Molybdopterin-converting factor from Helicobacter pylori 26695
Components
  • Molybdopterin converting factor, subunit 1 (MoaD)
  • Molybdopterin synthase catalytic subunit
KeywordsTRANSFERASE / MCSG / PSI-Biology / Structural Genomics / Midwest Center for Structural Genomics
Function / homology
Function and homology information


molybdopterin synthase / molybdopterin synthase activity / Mo-molybdopterin cofactor biosynthetic process / cytosol
Similarity search - Function
Molybdopterin biosynthesis MoaE subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Aldehyde Oxidoreductase; domain 3 / Beta-grasp domain / Beta-grasp domain superfamily ...Molybdopterin biosynthesis MoaE subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Aldehyde Oxidoreductase; domain 3 / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Molybdopterin converting factor, subunit 1 (MoaD) / Molybdopterin synthase catalytic subunit
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsNocek, B. / Stein, A. / Marshall, N. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Protein-protein complex of subunit 1 and 2 of Molybdopterin-converting factor from Helicobacter pylori 26695
Authors: Nocek, B. / Stein, A. / Marshall, N. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdopterin synthase catalytic subunit
B: Molybdopterin synthase catalytic subunit
C: Molybdopterin converting factor, subunit 1 (MoaD)
D: Molybdopterin converting factor, subunit 1 (MoaD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,18410
Polymers50,7444
Non-polymers4406
Water2,162120
1
A: Molybdopterin synthase catalytic subunit
D: Molybdopterin converting factor, subunit 1 (MoaD)
hetero molecules

A: Molybdopterin synthase catalytic subunit
D: Molybdopterin converting factor, subunit 1 (MoaD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,18410
Polymers50,7444
Non-polymers4406
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area8420 Å2
ΔGint-70 kcal/mol
Surface area18670 Å2
MethodPISA
2
A: Molybdopterin synthase catalytic subunit
D: Molybdopterin converting factor, subunit 1 (MoaD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5925
Polymers25,3722
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-29 kcal/mol
Surface area10520 Å2
MethodPISA
3
B: Molybdopterin synthase catalytic subunit
C: Molybdopterin converting factor, subunit 1 (MoaD)
hetero molecules

B: Molybdopterin synthase catalytic subunit
C: Molybdopterin converting factor, subunit 1 (MoaD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,18410
Polymers50,7444
Non-polymers4406
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area8990 Å2
ΔGint-85 kcal/mol
Surface area19230 Å2
MethodPISA
4
B: Molybdopterin synthase catalytic subunit
C: Molybdopterin converting factor, subunit 1 (MoaD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5925
Polymers25,3722
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-33 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.187, 127.582, 187.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11D-101-

HOH

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Components

#1: Protein Molybdopterin synthase catalytic subunit / MPT synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin-converting ...MPT synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin-converting factor large subunit / Molybdopterin-converting factor subunit 2


Mass: 16988.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: moaE, HP_0800 / Production host: Escherichia coli (E. coli) / References: UniProt: P56422, Transferases
#2: Protein Molybdopterin converting factor, subunit 1 (MoaD)


Mass: 8383.478 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0801 / Production host: Escherichia coli (E. coli) / References: UniProt: O25482
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 0.2 M Ammonium sulfate 25% Peg 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→28 Å / Num. obs: 41239 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 25
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
ARP/wARPmodel building
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28 Å / SU ML: 0.26 / σ(F): 2 / Phase error: 27.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1910 5.04 %
Rwork0.202 --
obs0.204 37921 91.1 %
all-39831 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.27 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.0801 Å2-0 Å2-0 Å2
2---1.8688 Å20 Å2
3----16.2113 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 26 120 3427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073404
X-RAY DIFFRACTIONf_angle_d0.9854603
X-RAY DIFFRACTIONf_dihedral_angle_d15.1771200
X-RAY DIFFRACTIONf_chiral_restr0.069518
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9023-1.94980.34641280.30992101X-RAY DIFFRACTION76
1.9498-2.00250.37871030.27922266X-RAY DIFFRACTION80
2.0025-2.06140.2831200.26222319X-RAY DIFFRACTION83
2.0614-2.1280.29451440.23442418X-RAY DIFFRACTION87
2.128-2.2040.28441220.20892544X-RAY DIFFRACTION90
2.204-2.29220.27391230.2092539X-RAY DIFFRACTION90
2.2922-2.39650.28961380.20792580X-RAY DIFFRACTION92
2.3965-2.52280.28461430.22162644X-RAY DIFFRACTION94
2.5228-2.68080.29361320.22052708X-RAY DIFFRACTION96
2.6808-2.88760.27161480.21262756X-RAY DIFFRACTION98
2.8876-3.1780.23331430.20362780X-RAY DIFFRACTION98
3.178-3.63730.2141470.19652803X-RAY DIFFRACTION99
3.6373-4.58030.20371660.16152821X-RAY DIFFRACTION99
4.5803-31.32840.20311530.18912732X-RAY DIFFRACTION93
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)
11.3534-0.42220.05210.8975-0.19830.9331-0.11390.00890.2507-0.0890.04590.2451-0.041-0.2426-0.14660.04070.1864-0.40010.1520.06820.189711.1731-4.056378.2405
20.5508-0.1619-0.34622.431-1.33973.693-0.06870.00390.0713-0.1610.17670.8998-0.0527-0.8795-0.14510.18090.0263-0.07260.47310.01680.60276.1646-2.408888.438
31.30611.5372-1.78322.4659-1.05444.11030.1790.10280.10740.02360.05090.42420.1448-0.51370.06210.1476-0.00710.01610.25860.02240.366812.7306-11.339495.4225
41.7819-0.2182-0.12.0693-0.90371.15330.0372-0.14510.2442-0.196-0.00780.1919-0.11650.0619-0.0640.15720.0173-0.02380.170.00020.276216.87228.710485.6623
50.9806-0.11860.28171.8788-0.55161.82480.03160.28320.0595-0.5972-0.18010.15970.17540.05960.060.38620.102-0.08670.2440.02110.2718.42011.89273.593
60.6614-0.86930.4153.5641-0.67324.22950.15950.1299-0.1868-0.5141-0.1209-0.05650.3548-0.2008-0.05490.35270.133-0.0620.2764-0.00880.353624.2383-13.224182.0791
70.13710.0160.1370.1886-0.41241.73390.10150.0843-0.1537-0.10470.00440.27870.35910.22810.0420.35440.23970.00460.35380.05490.258626.4307-16.123588.9709
80.2436-0.03680.29530.3008-0.47080.9082-0.0199-0.05140.0895-0.2442-0.17490.06870.1763-0.0104-0.16870.14650.0459-0.07860.207-0.0020.292914.8935-0.6483.1492
91.8243-0.10780.08761.4453-0.56031.47510.0721-0.079-0.12780.0516-0.0943-0.19690.25960.28040.09250.20420.0791-0.07120.25090.02420.343526.1211-9.578698.1946
101.62120.3310.68720.8595-0.34183.0578-0.29650.05480.195-0.3314-0.0577-0.1435-0.40820.19070.17870.2810.02-0.0140.2167-0.01630.239622.22054.331676.8406
115.1799-0.42043.30520.2479-1.18535.9955-0.0674-0.26560.5815-0.1141-0.1466-0.0255-0.7240.11720.12180.56170.0049-0.07220.2539-0.05790.337425.866611.319271.8465
123.327-1.6567-3.98632.34390.84426.4991-0.0303-0.34390.0265-0.2572-0.0064-0.5537-0.02010.26260.02160.45020.21370.08120.6015-0.01940.343835.3752-0.150966.1585
130.6371-1.0495-0.18742.10731.15423.50020.16090.1631-0.0547-0.2593-0.13420.024-0.4766-0.489-0.07120.32950.0743-0.01610.32850.08110.3157-3.894943.728978.3294
142.04680.027-1.01680.1893-0.29831.76740.1374-0.04470.62120.04460.07710.0518-0.4882-0.0337-0.13970.43840.10550.04680.2217-0.01120.3302-4.454647.055590.6176
150.9037-0.1638-0.95470.21170.05671.3616-0.0730.1358-0.17770-0.03010.0845-0.358-0.281-0.01090.13450.0615-0.00170.23030.01670.261-4.458339.078492.4962
162.7954-1.9003-1.50822.3017-0.55993.7335-0.0012-0.70880.17-0.03210.27710.43830.07460.3381-0.27710.3274-0.01110.08750.3624-0.01950.39519.933939.665677.5351
171.2504-0.62231.19391.0328-0.00692.51370.220.04180.1633-0.2042-0.01470.1458-0.0465-0.3347-0.0650.2897-0.0107-0.04930.32210.0120.2532-1.43936.214871.4968
181.12320.5764-0.26380.9482-0.28483.39290.04210.15880.18870.02460.19120.34910.0772-0.8020.10270.2461-0.1089-0.05310.4387-0.00530.3403-12.845929.829682.6567
190.706-0.02650.36210.96660.61451.2927-0.00970.00770.004-0.32080.00390.0522-0.259-0.1815-0.01270.20150.0106-0.02470.13690.00640.1923-0.617739.479282.9054
202.0544-1.61051.21751.80460.57335.18950.1005-0.1139-0.3377-0.1081-0.1566-0.0849-0.1377-0.21950.07140.165-0.0282-0.0510.21750.03110.2822-10.106130.681597.4163
210.52740.143-0.81610.6211-0.73031.6839-0.0117-0.0537-0.0397-0.1664-0.08160.06370.36050.0728-0.0970.26880.0195-0.03640.1999-0.0270.2799-1.382328.082282.6224
220.59560.9974-0.21071.85330.31632.00340.3329-0.0075-0.116-0.2986-0.0227-0.3388-0.02490.0748-0.12430.35140.0003-0.01110.2567-0.01430.296613.03437.34569.0115
232.92421.213-0.17711.4882-1.34082.3278-0.30270.03970.019-0.2457-0.21050.07950.42550.06690.11660.46340.1208-0.0780.29720.01220.28438.628725.83172.8794
246.55552.8462-4.1383.403-4.67276.4407-0.17010.2332-0.2288-0.3889-0.0133-0.0173-0.23810.06540.16260.8254-0.18620.07360.3619-0.10870.38510.161218.168563.4683
250.96130.4494-0.72382.0546-0.73520.6272-0.41071.0063-0.012-0.29210.35110.17220.3962-0.47440.04960.3864-0.09450.00390.5643-0.01420.243-4.611929.933456.2404
261.2295-0.5221-1.15731.8999-0.61841.8897-0.2540.47360.2189-0.2401-0.00130.0724-0.0626-0.36030.07270.43920.03810.00730.51310.07710.26911.2833.116253.5094
271.28790.86452.42575.7512-1.50986.4621-0.15710.501-0.21070.02120.30940.0980.6724-0.4474-0.22310.4409-0.2557-0.05560.83950.03050.3717-8.924524.527249.2086
281.8175-0.1652-0.86832.4978-0.85253.7750.120.0678-0.2824-0.1570.12430.06440.9587-0.0002-0.12851.1391-0.0576-0.06610.6822-0.18780.432-4.138717.269852.7586
291.0734-1.8757-2.14624.32324.7935.33140.06950.0980.09620.51420.3253-0.21460.2616-0.1329-0.14380.81070.0306-0.0510.6301-0.13020.37692.784721.494450.4948
301.74390.45390.51411.06480.07070.15690.18380.6351-0.0654-0.11160.037-0.39250.27460.3113-0.21390.62430.11480.01050.5518-0.07850.31777.187124.189959.1588
313.40940.25360.40390.17990.7317.34810.3343-0.1193-0.20830.37-0.09460.02911.0656-0.5142-0.12140.5291-0.17860.02430.52040.02620.2217-8.474523.922464.8728
322.8043-0.36812.26030.9867-1.07612.66940.29760.753-0.2748-0.53930.08090.03980.83130.2644-0.29640.723-0.2513-0.07671.0771-0.19710.6694-13.069119.59156.4556
331.5866-0.5607-1.25311.2615-0.53651.8922-0.10540.18240.1014-0.07670.0257-0.08440.3313-0.44440.13320.38090.0107-0.01980.3867-0.05080.2364-1.768828.563965.1876
340.3351-0.2006-0.4812.40951.68082.3130.0110.0888-0.0863-0.4626-0.1977-0.11380.33640.19110.00661.25960.1735-0.11310.29830.0519-0.182123.4808-3.581758.1393
351.7406-0.162-2.21890.0579-0.09234.9178-0.00810.0581-0.0499-0.2537-0.26070.21720.4764-0.07520.15811.0142-0.0315-0.01770.3818-0.00350.337821.72214.231857.3973
360.2815-0.3968-0.07621.59961.53861.9679-0.1049-0.00330.0248-0.55290.01980.0213-0.13150.03070.13391.3095-0.0130.02880.326-0.06920.390826.0839-5.431750.6067
370.0677-0.15710.12080.3539-0.27510.21590.08210.09960.1545-0.51910.0522-0.2186-0.19210.2742-0.03511.3028-0.00910.45110.86580.00840.278833.2121.411551.3605
380.5231-1.83660.69886.4983-2.29871.4068-0.3616-0.0305-0.1923-0.2079-0.3614-0.2050.97020.60310.58091.093-0.27460.16180.6510.0920.476630.76687.398158.5229
391.0332-0.00690.08541.13170.60022.95040.2754-0.0648-0.0595-0.00410.1078-0.05720.85920.53670.48750.91050.33410.23590.49640.04780.213330.18-5.710764.4577
402.18841.77752.08416.23810.96832.38790.0131-0.2332-0.1962-0.7728-0.45710.02020.2861-0.1630.17751.21750.36260.35590.7648-0.01410.55632.8751-13.046257.5523
410.582-0.09460.42381.7297-0.18871.66060.06530.0107-0.1866-0.21430.131-0.07820.80630.5971-0.00311.10360.14250.14460.5247-0.01180.139526.9204-8.154558.378
421.0013-0.68910.88092.55992.39495.1248-0.0649-0.05960.0639-0.3423-0.36810.3782-0.13870.29440.30860.5437-0.10120.08070.3253-0.01610.315225.83253.572571.4867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 0:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 10:16)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 17:30)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 31:40)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 41:59)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 60:64)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 65:70)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 71:95)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 96:103)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 104:128)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 129:136)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 137:144)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 0:9)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 10:20)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 21:38)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 39:44)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 45:57)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 58:68)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 69:93)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 94:102)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 103:118)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 119:132)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 133:138)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 139:145)
25X-RAY DIFFRACTION25(CHAIN C AND RESID 1:11)
26X-RAY DIFFRACTION26(CHAIN C AND RESID 12:16)
27X-RAY DIFFRACTION27(CHAIN C AND RESID 17:22)
28X-RAY DIFFRACTION28(CHAIN C AND RESID 23:28)
29X-RAY DIFFRACTION29(CHAIN C AND RESID 29:33)
30X-RAY DIFFRACTION30(CHAIN C AND RESID 34:43)
31X-RAY DIFFRACTION31(CHAIN C AND RESID 44:54)
32X-RAY DIFFRACTION32(CHAIN C AND RESID 55:61)
33X-RAY DIFFRACTION33(CHAIN C AND RESID 62:74)
34X-RAY DIFFRACTION34(CHAIN D AND RESID 3:9)
35X-RAY DIFFRACTION35(CHAIN D AND RESID 10:15)
36X-RAY DIFFRACTION36(CHAIN D AND RESID 16:24)
37X-RAY DIFFRACTION37(CHAIN D AND RESID 25:35)
38X-RAY DIFFRACTION38(CHAIN D AND RESID 36:40)
39X-RAY DIFFRACTION39(CHAIN D AND RESID 41:51)
40X-RAY DIFFRACTION40(CHAIN D AND RESID 52:61)
41X-RAY DIFFRACTION41(CHAIN D AND RESID 62:67)
42X-RAY DIFFRACTION42(CHAIN D AND RESID 68:74)

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