[English] 日本語
Yorodumi
- PDB-6yrm: Transaldolase variant T30A from T. acidophilum in complex with D-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yrm
TitleTransaldolase variant T30A from T. acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate
ComponentsProbable transaldolase
KeywordsTRANSFERASE / ALPHA-BETA BARREL / CONFORMATIONAL SELECTION / DOMAIN SWAPPING / TIM BARREL / SCHIFF BASE / Large-scale motions / Substrate binding / rate-determining product release
Function / homology
Function and homology information


transaldolase / transaldolase activity / aldehyde-lyase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Transaldolase type 3B, putative / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / FRUCTOSE -6-PHOSPHATE / Probable transaldolase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSautner, V. / Klaus, M. / Tittmann, K.
CitationJournal: To Be Published
Title: Large-scale motions underlie physical but not chemical steps in transaldolase mechanism: Substrate binding by conformational selection and rate-determining product release
Authors: Sautner, V. / Lietzow, T.H. / Klaus, M. / Funk, L.M. / Tittmann, K.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,50421
Polymers122,3235
Non-polymers2,18216
Water9,332518
1
A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules

A: Probable transaldolase
B: Probable transaldolase
C: Probable transaldolase
D: Probable transaldolase
E: Probable transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,00842
Polymers244,64510
Non-polymers4,36332
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area53120 Å2
ΔGint-381 kcal/mol
Surface area74930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.600, 172.270, 99.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-303-

GOL

21C-304-

ACT

31C-304-

ACT

-
Components

#1: Protein
Probable transaldolase


Mass: 24464.518 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: tal, Ta0616 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HKI3, transaldolase
#2: Chemical
ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 188 mM ammonium acetate (pH 4.4), 10% (w/v) PEG 6000, and 25% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→49.027 Å / Num. obs: 139170 / % possible obs: 99.2 % / Redundancy: 6.781 % / Biso Wilson estimate: 34.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.057 / Χ2: 1.025 / Net I/σ(I): 17.22 / Num. measured all: 943694 / Scaling rejects: 145
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.86.9292.4351.13216890.4342.6398.9
1.8-1.96.881.2212.13173450.7231.3298.8
1.9-26.8320.6713.65140670.8950.72698.9
2-2.56.8350.17911.59416710.9910.19499.5
2.5-36.7290.06325.88185680.9980.06899.8
3-56.5290.0347.38201060.9990.03299.2
5-106.5880.02464.0849900.9990.02699.3
10-205.6930.02166.436520.9990.02497.3
20-504.2560.02255.42820.9980.02578.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S0C

3s0c


Resolution: 1.7→49.027 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.14
RfactorNum. reflection% reflection
Rfree0.205 6957 5 %
Rwork0.1744 --
obs0.1759 139112 99.17 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 158.31 Å2 / Biso mean: 52.9923 Å2 / Biso min: 24.92 Å2
Refinement stepCycle: final / Resolution: 1.7→49.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8585 0 143 519 9247
Biso mean--43.84 50.86 -
Num. residues----1115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.71930.3912300.3529435898
1.7193-1.73950.34712270.3309430799
1.7395-1.76080.37952310.3265437799
1.7608-1.7830.3542290.3198435499
1.783-1.80650.36362290.3054436299
1.8065-1.83130.32042270.2913432899
1.8313-1.85740.32392290.2854434599
1.8574-1.88510.30922300.2654437399
1.8851-1.91460.3012280.264433399
1.9146-1.9460.32322310.2864437699
1.946-1.97960.31312280.2679434299
1.9796-2.01560.31382310.2461437999
2.0156-2.05430.28962310.2301438499
2.0543-2.09630.25182310.20484403100
2.0963-2.14180.24272310.2047438599
2.1418-2.19170.22612310.1925439499
2.1917-2.24650.25242310.18664375100
2.2465-2.30720.20752330.18274433100
2.3072-2.37510.20552340.17534445100
2.3751-2.45180.23942320.18034412100
2.4518-2.53940.19632330.17244433100
2.5394-2.6410.22182350.17284452100
2.641-2.76120.23012330.18744433100
2.7612-2.90680.22072340.1764441100
2.9068-3.08890.20062330.1775443899
3.0889-3.32730.21712330.1699441899
3.3273-3.66210.1862330.1586443499
3.6621-4.19170.14872360.1376448499
4.1917-5.28020.14572390.13084530100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.5099-1.25121.35647.76793.77932.6703-0.12850.4309-0.9313-0.09520.0028-0.02271.5909-0.49730.12091.0271-0.15940.19840.4862-0.11430.57073.9409-73.0795-0.6367
23.64420.08161.69763.52642.92345.2941-0.37230.4514-1.1398-0.71470.1263-0.53741.99150.302-0.04811.12440.02370.26530.5784-0.17170.737811.6568-73.245-8.2078
32.4570.4017-0.71883.92720.2765.3649-0.16490.5012-0.5105-0.617-0.0667-0.28080.6928-0.16350.22520.4986-0.00150.10690.5177-0.15940.367412.1744-60.0711-14.6416
45.05020.12626.79938.06121.93299.7371-0.03250.77940.2728-0.67170.1897-0.2964-0.930.154-0.15610.5669-0.01680.11060.587-0.02750.369612.8937-49.398-14.9013
52.74050.0484-0.90575.6044-0.09072.0866-0.06120.2896-0.0969-0.2278-0.0011-0.02610.1233-0.08140.06490.2628-0.01620.02760.3407-0.05170.28039.5974-51.8695-5.2982
64.5226-3.40151.86195.2352-3.01382.2819-0.0413-0.0673-0.1380.02780.06380.017-0.09720.0411-0.03870.2408-0.01810.01680.3153-0.05850.31289.6954-50.72948.1599
70.48180.9115-1.08935.7594-3.2373.8112-0.07890.0181-0.1749-0.06090.036-0.02290.1852-0.08130.0170.2112-0.02580.00910.3126-0.06790.34814.5269-57.41176.5199
83.22281.7636-4.7771.0769-2.33568.3266-0.5453-0.1111-0.6343-0.5855-0.0143-0.18921.31660.25150.54610.4471-0.01560.03870.3467-0.08830.45123.5994-68.99028.055
93.85093.57251.62613.33570.8695.04040.1642-0.8634-0.9325-0.1721-0.14530.9341.2531-0.7293-0.07810.9063-0.1048-0.03550.55060.02671.1806-13.8723-85.352521.4309
107.13050.4801-3.5788.05370.51785.3870.25490.4391-0.2023-0.6175-0.3135-0.62820.26390.58450.06020.47970.07680.05950.51320.04350.298318.0603-33.2651-10.915
112.79470.36080.54984.7370.25346.48870.15220.70240.3451-0.7062-0.2696-0.6641-0.47590.70320.0710.60380.05920.16510.65680.14320.438919.9572-23.057-13.9593
123.0015-0.5752-0.05890.7443-0.54252.95890.33660.71780.5373-0.464-0.23410.1262-0.7177-0.1296-0.09890.76120.05110.07990.51210.15370.38198.2166-15.6279-11.1454
135.4436-0.77710.67863.42120.06227.69370.3205-0.14120.9561-0.6587-0.26660.4718-1.1834-0.3934-0.10380.74020.1330.03680.46630.12430.51530.3514-10.8816-4.093
143.5681-0.0745-0.65322.97950.73011.17730.1440.35450.03-0.4732-0.08470.1444-0.3633-0.104-0.07620.49120.04850.01440.30730.03320.29213.3273-20.0333-0.4062
155.37680.6999-0.03492.2370.33890.74350.3013-0.1332-0.07090.028-0.1417-0.1479-0.11950.0467-0.09340.3861-0.01270.01050.2834-0.00220.26656.6414-27.526410.1218
165.3723-3.7289-1.95264.31130.91871.82680.20590.20570.0995-0.2825-0.1203-0.0172-0.15870.1059-0.07420.3034-0.0356-0.00370.2635-0.00380.22298.5694-32.34993.525
173.48920.60240.74918.5959-4.1073.48280.3440.48170.0696-0.6809-0.5808-1.09060.06970.5510.23050.34060.0040.04090.3818-0.02310.263717.6103-37.6142-2.202
186.00610.13682.34694.98333.73037.4633-0.02731.255-1.0265-0.22960.0575-0.44231.23850.7373-0.14630.64860.07020.15110.7608-0.15580.660224.2219-63.375-7.729
197.22650.62280.22368.88670.99333.2062-0.13780.67510.7203-0.4470.1005-0.3347-0.3790.27330.02660.73880.08130.00780.40090.15030.4661-8.0873-5.06978.3053
202.3894-1.20451.03025.2242-2.11491.0625-0.1272-0.11210.77410.1530.0406-0.0023-1.37970.10110.11491.04130.1439-0.01110.36010.05470.5952-15.75691.543412.569
214.0123-0.3598-0.85564.6352-0.56614.6655-0.0383-0.3230.3820.11410.14460.2325-0.7043-0.1271-0.07550.71410.21280.00620.36190.07540.4434-22.9949-5.97715.3363
221.6579-0.4938-0.95032.0448-0.78552.2520.01390.15420.1957-0.01120.07270.5965-0.7256-0.5315-0.10930.72990.2868-0.02130.47360.05320.5414-29.5738-7.128215.6086
232.0086-0.2247-0.62443.8544-0.10822.56680.03930.11270.1999-0.10970.05030.4367-0.3505-0.4874-0.10690.44380.18510.01710.39180.05690.3976-26.1813-16.944719.7403
243.7894.58893.68277.32196.37765.97090.08450.0148-0.03190.01480.057-0.0887-0.2345-0.026-0.15340.34310.07860.03760.24160.03910.2499-11.3396-22.970724.3271
253.17220.7909-0.61911.5911-0.49711.02080.02160.21780.2949-0.09370.0791-0.0039-0.3778-0.0833-0.10640.48120.06620.01310.28290.0320.3058-6.7243-16.755815.0909
265.75330.7808-0.90045.8471-4.06979.13910.05160.65570.5959-0.6852-0.0301-0.7955-1.06521.3854-0.11240.8343-0.17720.09430.59720.10180.664219.4549-11.0348-3.8299
274.0507-3.0149-3.12273.41921.58645.075-0.05830.17321.3631-0.1153-0.19691.0985-0.8156-1.01250.10310.50640.1628-0.05120.6574-0.07040.8967-38.0306-27.510930.9765
282.9088-1.48832.60426.9644-1.80912.3585-0.2103-0.90560.68531.0205-0.36870.7032-0.5783-1.01470.07940.49620.08350.04410.8062-0.20340.7551-42.5134-31.918936.6513
298.8302-4.73332.00067.5142-4.38518.23370.0976-0.82890.68860.62580.39981.1194-0.5899-0.8413-0.52180.39770.1493-0.00640.8153-0.12860.9646-49.9539-32.872131.8566
305.4549-0.07930.48214.87130.84161.6576-0.0346-0.2130.5054-0.1041-0.06880.6831-0.1291-0.5440.05280.20190.0421-0.03370.61110.01010.4964-44.9479-45.985228.9017
315.7231-3.04084.78216.0031-2.85144.13340.21370.3438-0.8865-0.14280.06650.40530.5195-0.3204-0.32210.27-0.02940.00090.49550.01040.548-40.1526-55.69626.1317
320.6091-0.6629-1.03024.08880.42522.2120.0356-0.0174-0.1148-0.1159-0.00530.079-0.0611-0.2654-0.04380.18860.0112-0.01380.39340.00890.3406-32.6506-48.308726.8418
330.8117-0.0129-0.10881.83222.00112.54520.0397-0.0873-0.03630.03150.1056-0.0984-0.1707-0.0042-0.16120.24640.0354-0.00510.33080.02020.3624-20.2319-43.957331.6513
340.93250.075-0.42295.0031.63111.54930.00950.05830.1073-0.0267-0.01970.1365-0.1689-0.16820.05890.23620.0786-0.00750.35780.03140.3129-24.0649-38.18327.6339
354.34194.3501-1.16727.89442.36823.75280.3269-0.33110.54060.3116-0.60771.2664-0.4186-0.38560.26940.35420.1259-0.01860.42460.0070.4219-28.2164-26.896832.0776
362.7836-2.25981.28296.8022-4.06132.43010.0420.19430.7045-0.1706-0.21840.3704-1.4906-0.31240.06921.15750.24210.02310.5114-0.06310.661-21.8352-0.805826.7821
373.7559-0.88481.62770.3458-0.83783.9408-0.0657-0.875-0.53250.0823-0.34650.98311.2393-1.18410.10340.6384-0.28870.2320.8207-0.2041.0507-28.3055-73.318925.0882
380.90630.5580.39291.2799-0.4810.95830.5941-0.2577-0.35750.1560.21970.51680.226-0.29370.89110.5493-0.85840.47650.7478-0.81.8162-32.1511-80.672518.7452
394.671-0.2159-0.01140.4804-1.18843.06530.0726-0.0471-0.92740.1652-0.45451.14770.7003-0.24660.15360.4919-0.23780.04920.5387-0.25940.936-21.5097-77.636414.4207
400.01650.0437-0.00620.0691-0.07810.315-0.1790.302-0.8185-0.1116-0.37530.95090.5803-0.72010.03430.5158-0.19880.02020.5784-0.33081.0191-19.8137-80.02158.339
413.71250.7807-0.10185.67840.70963.89790.01870.4732-0.4887-0.3863-0.18620.16780.2661-0.36270.10480.2758-0.03750.01720.3391-0.15190.458-12.1172-71.84969.1882
420.6858-1.4350.68755.6963-6.11029.3807-0.09450.0142-0.140.12570.02380.0834-0.0654-0.09670.10280.2214-0.01620.0010.2955-0.0480.4177-7.5581-61.541121.4638
433.10320.7303-3.47351.248-0.47664.6735-0.14780.1603-0.18150.01220.01680.08940.2552-0.25510.11070.1995-0.014-0.00930.3182-0.03730.3945-15.1109-60.186120.885
442.6256-0.9596-3.58473.89513.13256.5057-0.63670.37-0.8780.6084-0.3520.48871.023-1.13770.89320.3473-0.08260.09910.441-0.03920.5228-24.5355-62.398529.3938
457.6048-2.29091.7358.0064-0.62834.7772-0.2484-0.55070.43720.44060.24521.5699-0.2953-1.89750.02440.51760.01520.10730.99560.04130.7196-42.4185-46.559542.7196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )A1 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 52 )A20 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 90 )A53 - 90
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 102 )A91 - 102
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 132 )A103 - 132
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 157 )A133 - 157
7X-RAY DIFFRACTION7chain 'A' and (resid 158 through 180 )A158 - 180
8X-RAY DIFFRACTION8chain 'A' and (resid 181 through 198 )A181 - 198
9X-RAY DIFFRACTION9chain 'A' and (resid 199 through 223 )A199 - 223
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 19 )B1 - 19
11X-RAY DIFFRACTION11chain 'B' and (resid 20 through 52 )B20 - 52
12X-RAY DIFFRACTION12chain 'B' and (resid 53 through 90 )B53 - 90
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 102 )B91 - 102
14X-RAY DIFFRACTION14chain 'B' and (resid 103 through 132 )B103 - 132
15X-RAY DIFFRACTION15chain 'B' and (resid 133 through 157 )B133 - 157
16X-RAY DIFFRACTION16chain 'B' and (resid 158 through 180 )B158 - 180
17X-RAY DIFFRACTION17chain 'B' and (resid 181 through 198 )B181 - 198
18X-RAY DIFFRACTION18chain 'B' and (resid 199 through 223 )B199 - 223
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 19 )C1 - 19
20X-RAY DIFFRACTION20chain 'C' and (resid 20 through 52 )C20 - 52
21X-RAY DIFFRACTION21chain 'C' and (resid 53 through 65 )C53 - 65
22X-RAY DIFFRACTION22chain 'C' and (resid 66 through 90 )C66 - 90
23X-RAY DIFFRACTION23chain 'C' and (resid 91 through 132 )C91 - 132
24X-RAY DIFFRACTION24chain 'C' and (resid 133 through 156 )C133 - 156
25X-RAY DIFFRACTION25chain 'C' and (resid 157 through 198 )C157 - 198
26X-RAY DIFFRACTION26chain 'C' and (resid 199 through 223 )C199 - 223
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 18 )D1 - 18
28X-RAY DIFFRACTION28chain 'D' and (resid 19 through 41 )D19 - 41
29X-RAY DIFFRACTION29chain 'D' and (resid 42 through 52 )D42 - 52
30X-RAY DIFFRACTION30chain 'D' and (resid 53 through 90 )D53 - 90
31X-RAY DIFFRACTION31chain 'D' and (resid 91 through 102 )D91 - 102
32X-RAY DIFFRACTION32chain 'D' and (resid 103 through 132 )D103 - 132
33X-RAY DIFFRACTION33chain 'D' and (resid 133 through 156 )D133 - 156
34X-RAY DIFFRACTION34chain 'D' and (resid 157 through 180 )D157 - 180
35X-RAY DIFFRACTION35chain 'D' and (resid 181 through 198 )D181 - 198
36X-RAY DIFFRACTION36chain 'D' and (resid 199 through 223 )D199 - 223
37X-RAY DIFFRACTION37chain 'E' and (resid 1 through 41 )E1 - 41
38X-RAY DIFFRACTION38chain 'E' and (resid 42 through 52 )E42 - 52
39X-RAY DIFFRACTION39chain 'E' and (resid 53 through 65 )E53 - 65
40X-RAY DIFFRACTION40chain 'E' and (resid 66 through 90 )E66 - 90
41X-RAY DIFFRACTION41chain 'E' and (resid 91 through 132 )E91 - 132
42X-RAY DIFFRACTION42chain 'E' and (resid 133 through 156 )E133 - 156
43X-RAY DIFFRACTION43chain 'E' and (resid 157 through 180 )E157 - 180
44X-RAY DIFFRACTION44chain 'E' and (resid 181 through 198 )E181 - 198
45X-RAY DIFFRACTION45chain 'E' and (resid 199 through 223 )E199 - 223

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more