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- PDB-2g7z: Conserved DegV-like Protein of Unknown Function from Streptococcu... -

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Basic information

Entry
Database: PDB / ID: 2g7z
TitleConserved DegV-like Protein of Unknown Function from Streptococcus pyogenes M1 GAS Binds Long-chain Fatty Acids
Componentsconserved hypothetical protein SPy1493
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Long-Fatty acid binding protein / Lipid binding protein / PSI / MCSG / Hypothetical protein / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Rossmann fold - #10170 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID / DegV domain-containing protein SPy_1493/M5005_Spy1226
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsNocek, B. / Volkart, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Conserved hypothetical protein from Streptococcus pyogenes M1 GAS discloses long-fatty acid (heptadecanoic acid) binding function
Authors: Nocek, B. / Volkart, L. / Clancy, S. / Joachimiak, A.
History
DepositionMar 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT OF THE PROTEIN IS UNKNOWN, ALTHOUGH THE CRYSTALLOGRAPHIC ANALYSIS SUGGESTS THAT MONOMER IS LIKELY RELEVANT OLIGOMERIC FORM.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein SPy1493
B: conserved hypothetical protein SPy1493
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,43426
Polymers61,1742
Non-polymers2,26024
Water8,305461
1
A: conserved hypothetical protein SPy1493
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,88516
Polymers30,5871
Non-polymers1,29815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: conserved hypothetical protein SPy1493
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,54910
Polymers30,5871
Non-polymers9629
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: conserved hypothetical protein SPy1493
hetero molecules

B: conserved hypothetical protein SPy1493
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,43426
Polymers61,1742
Non-polymers2,26024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_466x-1/2,-y+3/2,-z+11
Buried area5270 Å2
ΔGint-376 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.126, 74.093, 128.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis entry contains 2 protein molecules in the crystallographic asymmetric unit. The biological unit of the protein is unknown, although the crystallographic analysis suggests that monomer is likely relevant oligomeric form

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein conserved hypothetical protein SPy1493


Mass: 30587.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M1 GAS / Plasmid: PMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P67372

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Non-polymers , 6 types, 485 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HXA / DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID / Docosahexaenoic acid


Mass: 328.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H32O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 % PEG 3k, 0.2 M Zn Acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2005
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. all: 45357 / Num. obs: 45131 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 19.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.599 / Rsym value: 0.021 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.039 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20714 2265 5 %RANDOM
Rwork0.16548 ---
obs0.16756 42608 99.45 %-
all-44873 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.701 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 0 89 461 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9955772
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52325.211142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61815783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.861514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022998
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22145
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22967
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2375
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1880.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0970.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7411.52845
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11924436
X-RAY DIFFRACTIONr_scbond_it2.32931636
X-RAY DIFFRACTIONr_scangle_it3.1794.51335
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 155 -
Rwork0.202 2942 -
obs--94.65 %
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)
113.86415.55288.656285.07294.15832.6353-1.95740.86350.4123-3.97521.6792-1.4496-1.47451.11130.27820.0574-0.14410.01190.0979-0.0248-0.016465.42949.720738.2604
20.59870.6446-0.13670.7506-0.37460.94560.0533-0.004-0.06980.0278-0.008-0.05360.04790.0522-0.04530.03390.02070.0043-0.0046-0.0066-0.007150.9332.758239.3588
319.893610.41584.967722.7047-5.035815.14730.1868-0.7408-1.16840.4003-0.1308-0.55140.2554-0.331-0.0560.05570.00280.0086-0.08030.07-0.034141.714717.871853.7761
43.61312.67271.89014.8552.34462.4314-0.00750.1007-0.0654-0.21050.0637-0.2034-0.1240.0668-0.05620.04110.01840.031-0.0166-0.0039-0.028445.458520.86941.2753
50.66250.7329-0.17411.40380.20530.5754-0.0143-0.1422-0.04150.1194-0.08930.03920.0874-0.02560.10360.05740.00030.0047-0.0341-0.0139-0.011940.875824.159950.2681
615.95653.5982-5.95083.4232-0.26542.6629-0.0156-0.3162-0.16710.2703-0.0935-0.2830.09860.22530.10910.02390.0076-0.04310.0229-0.0148-0.030960.866737.762150.0126
74.00592.1204-0.83941.204-0.29660.44310.0009-0.048-0.04680.04320.0010.0519-0.14740.0578-0.00190.0458-0.0043-0.003-0.0005-0.0218-0.036349.130240.810746.0475
812.5992.48324.8643.47270.20652.0675-0.3191-0.11370.37580.45770.1740.1736-0.4094-0.17880.14510.08140.0040.0189-0.0134-0.006-0.018845.552141.049852.6217
90.79890.0420.49550.36340.1440.8031-0.0289-0.04850.0509-0.0752-0.02150.042-0.09730.02260.05040.04260.00570.007-0.0075-0.0033-0.018247.401141.597244.6608
101.87451.3911-0.30131.8129-0.16790.6898-0.14720.2150.0664-0.22410.1578-0.0512-0.00190.1508-0.01060.0624-0.020.01020.0073-0.0119-0.028955.951445.278933.2939
1115.4282.76612.08012.18290.22813.5704-0.0093-0.01820.2916-0.1884-0.02220.0811-0.10240.05580.03150.104-0.00870.0195-0.08510.0036-0.013449.200650.9136.1838
121.42811.8154-0.51233.0292-0.04550.6922-0.07360.01130.1096-0.2460.05090.1596-0.0082-0.10.02270.03380.0275-0.0273-0.02090.0092-0.000831.849338.486136.357
132.1889-2.1864-0.31873.4696-1.66685.69280.0386-0.1332-0.06780.07760.08990.27810.2164-0.2961-0.1285-0.0017-0.00950.0219-0.0208-0.01220.005425.85831.49548.659
145.59122.44454.21272.33733.75826.069-0.1226-0.05380.2639-0.00090.12940.1589-0.0303-0.0391-0.0068-0.00930.00240.0282-0.04070.010.019525.450538.730140.6236
150.16590.779-1.068810.7773-5.35496.9035-0.00430.10010.0815-0.35960.08610.74890.2143-0.4495-0.0818-0.0219-0.059-0.10340.00450.02150.055621.081433.653329.4714
160.5004-1.38770.32344.4403-1.58681.01310.07650-0.0664-0.20560.00440.10440.0276-0.0867-0.08090.1103-0.0096-0.0299-0.0469-0.0113-0.031833.49439.912525.9136
172.202-1.86050.71864.2955-5.09089.51370.05990.1016-0.3956-0.3144-0.01720.27670.2712-0.0677-0.04270.102-0.0317-0.0579-0.0874-0.0388-0.015631.165424.490528.4098
1811.94712.9225.966815.12926.360614.7776-0.0178-0.0694-0.0672-1.2521-0.14830.26130.0818-0.56540.16610.2752-0.0007-0.0858-0.1337-0.0396-0.164530.27634.123719.7965
190.5046-0.00950.25572.7391-0.55075.3026-0.0544-0.02960.0323-0.2872-0.0174-0.00830.08680.15120.07180.041-0.0095-0.015-0.0449-0.0151-0.001238.775129.406831.9924
200.39650.551-0.66161.9602-0.61861.1797-0.08140.02030.0335-0.30860.0160.12590.1702-0.06250.06540.0501-0.0031-0.0235-0.0177-0.0024-0.010933.618934.199934.516
21111.2756-25.6133-1.40354.903414.11116.52810.28823.2892-0.8328-0.5823-0.3217-0.81920.37050.63560.03350.11420.078-0.015-0.04510.0211-0.110967.157327.147870.6672
220.7882-0.8305-0.42970.96350.2130.8845-0.0263-0.0264-0.0410.07710.05930.05330.0843-0.0986-0.0330.0195-0.01220.00120.01420.0004-0.01148.869843.4473.9727
231.79421.27182.20762.69322.20427.0730.01120.0885-0.06340.0437-0.09470.17390.11-0.20520.0835-0.0319-0.01730.01910.0047-0.0180.011440.242846.243977.6476
241.23370.13060.69166.47563.2836.42140.0217-0.00250.1063-0.08170.0264-0.27850.044-0.1352-0.048-0.03230.0038-0.02160.0303-0.0237-0.01335.455954.694773.4243
252.9006-1.77350.49611.640.05080.6644-0.0787-0.13440.11230.1879-0.0158-0.0607-0.0126-0.1430.09450.01540.0118-0.00840.0582-0.004-0.045445.239350.63985.1425
262.2203-3.9011.25618.1243.13573.24320.0883-0.2128-0.32730.5082-0.21350.19110.1341-0.39070.12520.0589-0.019-0.0033-0.01420.0319-0.035255.759532.028982.7915
271.5416-1.9152-0.0933.20280.7180.4464-0.0236-0.04170.078-0.01780.0636-0.06250.04790.0722-0.040.0383-0.0122-0.00120.00550.0096-0.026159.490244.143278.9587
280.1323-0.1840.60721.0215-0.87742.78840.0060.01950.04480.1731-0.0052-0.13750.00190.0945-0.00080.009-0.002-0.00620.0135-0.0068-0.004562.37941.756283.6777
290.0916-0.36160.06832.7465-0.06690.0823-0.00390.04960.0081-0.0682-0.025-0.00880.02010.11320.02890.0209-0.00670.00120.04670.0005-0.020857.762147.790467.1026
300.5769-0.4492-0.14481.6269-0.09280.77650.04470.10220.0442-0.1713-0.0495-0.15810.01950.15470.0049-0.02010.0003-0.00520.0507-0.0029-0.01765.232346.751167.0043
312.0001-0.41251.28421.9088-0.41655.0005-0.0453-0.16080.14270.12570.0240.029-0.1692-0.13040.02140.0031-0.00340.004-0.0434-0.02810.002349.314666.512179.5207
325.9784-16.0885-9.602248.201619.745422.9948-1.33451.82940.5516-0.5396-0.50340.2983-0.7255-0.72931.8379-0.0111-0.10430.2070.0668-0.03060.142949.617274.680474.9133
331.274-0.93152.99484.9366-2.29047.04230.09930.1487-0.00540.0581-0.103-0.3533-0.0990.02710.0037-0.0026-0.01110.0085-0.0493-0.01220.022857.97866.349573.1354
3435.27540.908717.24963.03911.973416.1144-0.2331-0.63612.25910.1005-0.29060.0521-0.7971-0.6640.5237-0.02050.03620.0602-0.10740.04590.109949.623374.767167.3066
3517.7238-3.8312-7.98151.5223.08256.2490.00230.85330.57620.1083-0.0565-0.1328-0.3257-0.33920.05420.02770.04660.0194-0.00040.13710.011153.596669.796659.4172
364.78111.7265-1.67040.6929-0.5090.71140.04510.39190.210.07260.1040.0709-0.0507-0.0458-0.1491-0.02180.0183-0.01040.12360.0264-0.034660.301359.37357.1801
374.94252.7147-3.04111.5204-1.15610.9035-0.06590.3050.2937-0.01510.04750.3141-0.0288-0.39390.0185-0.04630.0452-0.03990.06840.03810.010643.038760.875661.2126
3817.5054-9.202810.233316.5722-13.883214.78150.33961.1111-0.39160.1327-0.31230.5562-0.48030.207-0.0273-0.0853-0.0263-0.04660.24910.046-0.139952.844562.234151.8868
392.0390.1687-0.28081.1283-0.34725.13570.010.1960.0023-0.0336-0.03890.02050.2775-0.02460.0289-0.01930.0054-0.02720.02470.0081-0.013547.938453.858964.1829
402.9879-0.6355-1.12310.33120.63741.2321-0.00750.23030.0509-0.0414-0.07980.0133-0.0427-0.09160.08720.0091-0.0016-0.02170.01950.0181-0.015452.607459.068266.7066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 33 - 6
2X-RAY DIFFRACTION2AA4 - 317 - 34
3X-RAY DIFFRACTION3AA32 - 3835 - 41
4X-RAY DIFFRACTION4AA39 - 4842 - 51
5X-RAY DIFFRACTION5AA49 - 7252 - 75
6X-RAY DIFFRACTION6AA73 - 7976 - 82
7X-RAY DIFFRACTION7AA80 - 9783 - 100
8X-RAY DIFFRACTION8AA98 - 101101 - 104
9X-RAY DIFFRACTION9AA102 - 129105 - 132
10X-RAY DIFFRACTION10AA130 - 141133 - 144
11X-RAY DIFFRACTION11AA142 - 150145 - 153
12X-RAY DIFFRACTION12AA151 - 164154 - 167
13X-RAY DIFFRACTION13AA165 - 185168 - 188
14X-RAY DIFFRACTION14AA186 - 200189 - 203
15X-RAY DIFFRACTION15AA201 - 218204 - 221
16X-RAY DIFFRACTION16AA219 - 232222 - 235
17X-RAY DIFFRACTION17AA233 - 243236 - 246
18X-RAY DIFFRACTION18AA244 - 250247 - 253
19X-RAY DIFFRACTION19AA251 - 264254 - 267
20X-RAY DIFFRACTION20AA265 - 279268 - 282
21X-RAY DIFFRACTION21BB0 - 33 - 6
22X-RAY DIFFRACTION22BB4 - 367 - 39
23X-RAY DIFFRACTION23BB37 - 4540 - 48
24X-RAY DIFFRACTION24BB46 - 5449 - 57
25X-RAY DIFFRACTION25BB55 - 7158 - 74
26X-RAY DIFFRACTION26BB72 - 7975 - 82
27X-RAY DIFFRACTION27BB80 - 9983 - 102
28X-RAY DIFFRACTION28BB100 - 118103 - 121
29X-RAY DIFFRACTION29BB119 - 133122 - 136
30X-RAY DIFFRACTION30BB134 - 159137 - 162
31X-RAY DIFFRACTION31BB160 - 177163 - 180
32X-RAY DIFFRACTION32BB178 - 186181 - 189
33X-RAY DIFFRACTION33BB187 - 199190 - 202
34X-RAY DIFFRACTION34BB200 - 206203 - 209
35X-RAY DIFFRACTION35BB207 - 218210 - 221
36X-RAY DIFFRACTION36BB219 - 231222 - 234
37X-RAY DIFFRACTION37BB232 - 243235 - 246
38X-RAY DIFFRACTION38BB244 - 250247 - 253
39X-RAY DIFFRACTION39BB251 - 264254 - 267
40X-RAY DIFFRACTION40BB265 - 279268 - 282

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