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- PDB-9kyr: GH57 family amylopullulanase from Aquifex aeolicus D352N mutant c... -

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Basic information

Entry
Database: PDB / ID: 9kyr
TitleGH57 family amylopullulanase from Aquifex aeolicus D352N mutant complex with gama-cyclodextrin
ComponentsGlycoside hydrolase family 57 N-terminal domain-containing protein
KeywordsHYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus / cyclodextrin
Function / homology
Function and homology information


catalytic activity / carbohydrate metabolic process
Similarity search - Function
: / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
gamma-cyclodextrin / DI(HYDROXYETHYL)ETHER / Glycoside hydrolase family 57 N-terminal domain-containing protein
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsZhu, Z.M. / Wang, W.W. / Yu, F. / Li, M.J. / Xu, Q. / Zhou, H. / Huang, L.Q. / Wang, Q.S.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: J.Struct.Biol. / Year: 2025
Title: Mechanistic insights into cyclodextrins as substrates and inhibitors of GH57 family amylopullulanase from Aquifex aeolicus.
Authors: Zhu, Z. / Li, M. / Xu, Q. / Huang, L. / Zhou, H. / Wang, W. / Wang, Q. / Yu, F.
History
DepositionDec 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 57 N-terminal domain-containing protein
B: Glycoside hydrolase family 57 N-terminal domain-containing protein
C: Glycoside hydrolase family 57 N-terminal domain-containing protein
D: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,68125
Polymers229,0094
Non-polymers6,67221
Water11,620645
1
A: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24210
Polymers57,2521
Non-polymers1,9909
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0448
Polymers57,2521
Non-polymers1,7927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7364
Polymers57,2521
Non-polymers1,4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6593
Polymers57,2521
Non-polymers1,4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.830, 61.530, 195.400
Angle α, β, γ (deg.)83.94, 88.85, 89.09
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Glycoside hydrolase family 57 N-terminal domain-containing protein


Mass: 57252.250 Da / Num. of mol.: 4 / Mutation: D352N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: aq_720 / Production host: Escherichia coli (E. coli) / References: UniProt: O66934
#2: Polysaccharide
Cyclooctakis-(1-4)-(alpha-D-glucopyranose)


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1315.142 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: gamma-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,8,8/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1/a1-h4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0

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Non-polymers , 4 types, 662 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 338 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium citrate, pH 4.2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.89→64.76 Å / Num. obs: 143351 / % possible obs: 94.7 % / Redundancy: 3.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.116 / Rrim(I) all: 0.217 / Χ2: 0.92 / Net I/σ(I): 5.4 / Num. measured all: 492924
Reflection shellResolution: 1.89→1.94 Å / % possible obs: 92.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 2.21 / Num. measured all: 35725 / Num. unique obs: 10495 / CC1/2: 0.32 / Rpim(I) all: 1.396 / Rrim(I) all: 2.622 / Χ2: 0.96 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→24.329 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 7281 5.09 %
Rwork0.1926 --
obs0.1948 143024 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→24.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16088 0 444 645 17177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817040
X-RAY DIFFRACTIONf_angle_d0.95523086
X-RAY DIFFRACTIONf_dihedral_angle_d5.69814169
X-RAY DIFFRACTIONf_chiral_restr0.0532500
X-RAY DIFFRACTIONf_plane_restr0.0052846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.91150.40122250.37414428X-RAY DIFFRACTION91
1.9115-1.9340.42382120.35694400X-RAY DIFFRACTION91
1.934-1.95750.32972280.31564516X-RAY DIFFRACTION94
1.9575-1.98230.33162320.29294624X-RAY DIFFRACTION96
1.9823-2.00840.3092370.28154531X-RAY DIFFRACTION95
2.0084-2.03590.32792420.2784579X-RAY DIFFRACTION94
2.0359-2.06490.34862250.28974438X-RAY DIFFRACTION94
2.0649-2.09570.33192570.26324486X-RAY DIFFRACTION95
2.0957-2.12850.26042300.23584653X-RAY DIFFRACTION96
2.1285-2.16330.27672250.23594584X-RAY DIFFRACTION95
2.1633-2.20060.26972510.24084586X-RAY DIFFRACTION97
2.2006-2.24060.29012200.25214497X-RAY DIFFRACTION94
2.2406-2.28370.32492280.24044468X-RAY DIFFRACTION92
2.2837-2.33030.25132130.2214583X-RAY DIFFRACTION97
2.3303-2.38090.28712630.21654613X-RAY DIFFRACTION96
2.3809-2.43620.29372290.22334551X-RAY DIFFRACTION96
2.4362-2.49710.27062540.20674615X-RAY DIFFRACTION97
2.4971-2.56450.25632390.20444630X-RAY DIFFRACTION95
2.5645-2.63990.27732560.19824538X-RAY DIFFRACTION96
2.6399-2.7250.24332880.19374528X-RAY DIFFRACTION95
2.725-2.82230.24242310.20114608X-RAY DIFFRACTION97
2.8223-2.93510.25362540.19584583X-RAY DIFFRACTION95
2.9351-3.06840.26042880.19354491X-RAY DIFFRACTION96
3.0684-3.22980.25092340.18614506X-RAY DIFFRACTION94
3.2298-3.43170.23042260.17544446X-RAY DIFFRACTION92
3.4317-3.69580.19172600.16384324X-RAY DIFFRACTION91
3.6958-4.06620.18712720.14384378X-RAY DIFFRACTION92
4.0662-4.6510.16392890.13444417X-RAY DIFFRACTION94
4.651-5.84630.17062380.14444589X-RAY DIFFRACTION96
5.8463-24.3290.19212350.15954553X-RAY DIFFRACTION95
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)
10.2879-0.0185-0.03131.18470.29191.9064-0.00260.0211-0.0274-0.0806-0.03390.14730.1681-0.1480.04330.1353-0.05030.00750.1681-0.00030.2231-24.1182-33.103226.7128
20.97870.00120.15941.94580.95112.46460.06110.1692-0.0461-0.57240.0817-0.2992-0.00830.3973-0.10010.3333-0.0280.05760.3199-0.00340.2961-11.265-44.50710.382
30.47530.0656-0.10891.91810.64750.9939-0.03550.0065-0.10860.11950.01510.060.3005-0.07240.01240.204-0.0414-0.00510.18350.01350.2242-22.4322-43.514525.1358
40.65720.2701-0.8851.4566-0.5021.34760.01070.07120.1541-0.1888-0.0180.1415-0.088-0.0002-0.03730.1923-0.0066-0.02150.22440.00630.2431-26.2745-9.904724.8383
51.61910.8390.08851.14170.16741.2094-0.1013-0.16450.02350.1554-0.00940.0219-0.1684-0.25290.10840.1354-0.00720.0150.25430.0040.2314-26.3861-13.712835.7028
60.8259-0.4780.37382.1235-0.19071.1589-0.03250.12040.05240.2306-0.0231-0.1752-0.29160.1250.0230.142-0.04950.01030.23080.01620.2224-11.9123-16.604640.5962
70.74880.57360.09692.53021.62173.13210.112-0.0644-0.04420.37710.0204-0.16030.1688-0.0418-0.12260.1705-0.0197-0.01560.20050.02340.1991-11.9163-29.861344.4339
80.99810.0335-0.11521.3710.14492.24220.02330.04180.029-0.2529-0.0424-0.1491-0.21440.08030.030.2301-0.02110.00080.20.02080.2537-17.7845-9.495822.0654
91.41350.0696-0.02443.35750.28082.687-0.0103-0.0632-0.1464-0.3289-0.0290.0551-0.0888-0.03560.07720.202-0.0159-0.030.21260.02410.1857-23.7811-19.695812.2803
100.5406-0.11290.25151.79510.19430.51430.08420.08040.040.0263-0.05540.071-0.1531-0.0957-0.01390.24780.0560.0040.2519-0.00060.1726-28.1418-29.343-21.0009
110.4309-0.42210.30511.70361.25672.9012-0.06460.04250.05620.16340.1577-0.42980.30950.6154-0.11210.2974-0.0029-0.00870.3666-0.01250.3016-10.7156-20.4573-10.592
120.5454-0.01740.37821.32910.72171.0922-0.00420.05850.1301-0.2351-0.08990.1167-0.3439-0.06810.08020.37420.07620.01460.2960.00960.2382-26.304-20.1874-21.442
131.0721-0.54460.5632.0678-0.21031.71120.13970.0839-0.1837-0.044-0.16690.19590.3393-0.01540.04630.28430.01160.01350.2464-0.03710.2341-31.1098-53.7607-20.3479
141.6234-0.3459-0.00231.63150.63041.67040.07690.1632-0.0086-0.121-0.14750.2969-0.0503-0.30330.08790.29680.0416-0.07580.3381-0.03180.2458-33.0979-49.8042-31.111
151.3770.66340.03492.06340.36971.2177-0.07390.2041-0.0619-0.47580.0215-0.01490.00280.09080.00860.34810.1065-0.03010.346-0.01530.1835-19.654-47.3653-38.4683
161.2611-0.15870.51221.71190.59781.80480.10920.25740.0075-0.3977-0.0451-0.0153-0.1460.203-0.08570.39260.12590.01840.39870.01540.2385-16.0394-35.9225-41.1944
171.1952-0.29360.24822.30980.64181.73110.11430.48090.1422-0.5038-0.07040.1509-0.03260.0482-0.05310.42010.14660.00070.4230.03330.2237-24.0733-32.4333-43.6477
181.17280.13750.0562.2693-0.61291.64240.0059-0.0687-0.1220.1451-0.119-0.1038-0.09890.28580.13610.27430.0421-0.0230.2471-0.03230.2368-22.2248-54.362-19.2125
191.85760.59060.32683.48850.00451.83920.0482-0.05710.04620.448-0.0344-0.0491-0.0163-0.06050.02680.32260.0354-0.01230.2531-0.00280.1788-25.9776-44.0714-8.5975
200.857-0.4733-0.123.33330.88771.0224-0.1164-0.0232-0.1344-0.21060.03020.3199-0.0252-0.26520.07460.23470.0006-0.02450.2630.00640.2159-9.5169-15.8909-68.3205
210.5459-0.4265-0.10081.38970.81591.93380.13160.2098-0.0212-0.8452-0.04790.1595-0.1151-0.12230.03230.63070.0115-0.04070.3350.01210.2778-4.6034-22.5323-89.7856
220.6096-0.2365-0.23321.33361.31131.374-0.17950.011-0.2879-0.5940.2317-0.46850.14760.5525-0.13480.47850.02790.10650.4402-0.03770.35078.9576-28.4179-83.145
231.43650.0777-0.15822.9475-0.03992.14680.039-0.0235-0.185-0.2696-0.02130.28590.5655-0.2152-0.01110.3728-0.0229-0.06310.25510.01370.2916-6.9634-30.8557-76.2457
241.5872-0.8907-0.81742.08871.06172.12590.23250.05310.3308-0.5635-0.10410.0112-0.5931-0.0654-0.14390.54250.0874-0.04640.3255-0.00580.2743-7.61045.6725-68.469
251.5946-0.5659-0.13592.22680.89522.3423-0.021-0.1882-0.3314-0.1817-0.09860.7264-0.3588-0.43550.06230.29730.0975-0.07570.3574-0.03510.3913-15.9371-0.0994-62.0838
260.4271-0.5106-0.54451.2760.02561.2144-0.0772-0.04820.12580.26540.1598-0.3498-0.05940.1664-0.10410.26590.0457-0.09870.3818-0.07040.32531.1431-2.7689-53.6263
270.85070.3238-0.90871.46430.80211.8766-0.1362-0.3356-0.07270.51460.3469-0.45880.25260.5068-0.16160.42670.1343-0.12490.4635-0.05160.3264.4693-14.4216-53.0434
280.79970.40380.0862.21150.44321.7378-0.188-0.2903-0.17440.76370.21630.09260.2983-0.0059-0.05760.48140.1032-0.03430.4210.01830.2711-3.3259-18.0673-50.3095
291.838-0.5361-0.87032.2959-0.97982.42350.28210.03290.2233-0.8345-0.0113-0.3339-0.68080.4335-0.06260.72550.04150.03970.2419-0.00460.3209-2.4317.1134-70.7216
301.3717-0.3797-0.38173.3049-0.08972.14430.40280.13470.0478-1.0999-0.30820.1117-0.608-0.222-0.02110.86580.1479-0.06920.3503-0.00990.2604-8.2657-0.9909-83.0173
310.66980.12470.04131.9688-0.37910.7086-0.0267-0.06250.0470.26640.05530.0839-0.0466-0.1922-0.03160.19770.00930.0250.23590.00020.2137-4.7833-46.95573.7067
320.2095-0.4023-0.18641.36350.50252.5069-0.0441-0.41710.08550.85650.1183-0.4388-0.02960.4838-0.01740.65850.041-0.12490.411-0.04450.35158.2315-37.911191.9932
330.2299-0.0837-0.041.4867-0.06041.1956-0.021-0.05080.06340.28460.05390.011-0.3794-0.1793-0.0490.30560.0280.02830.25160.00340.2631-3.5075-36.832477.594
341.3208-1.00140.45572.6424-0.25411.85490.0138-0.0111-0.24520.09440.0820.30970.368-0.1563-0.04390.2394-0.050.03650.22980.02330.2265-6.7728-70.155472.2158
351.1441-1.315-0.2631.7067-0.09471.47750.06380.15720.02250.0301-0.08250.22950.1987-0.11870.00440.1865-0.05730.01170.27850.00960.2601-7.0399-64.578762.13
360.90670.70930.17112.0434-0.09340.8578-0.0506-0.1534-0.0951-0.2711-0.0221-0.35360.0180.0070.01420.1713-0.02050.03290.277-0.01070.28687.3688-60.641657.6989
370.8856-0.6050.81871.41680.08882.40090.00660.020.1199-0.22640.0162-0.30260.06450.2962-0.02990.148-0.04750.06150.21740.00430.301910.7812-48.875357.4625
380.4066-0.44720.04332.0489-0.39461.7909-0.05150.11250.0419-0.38720.0901-0.0167-0.11-0.0305-0.06560.0845-0.01610.04620.22870.01610.21722.8791-50.084554.2037
392.1494-0.17510.01562.2662-0.24412.6571-0.0199-0.3389-0.11170.6696-0.0597-0.31120.06870.37760.06060.33640.0065-0.04850.225500.232.0047-70.531180.2166
401.4353-0.0232-0.46193.46260.50112.68930.0181-0.09120.19370.61570.0843-0.03320.1551-0.0951-0.060.34570.02490.00420.18080.02410.1723-4.0947-62.444486.1883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 200 )
4X-RAY DIFFRACTION4chain 'A' and (resid 201 through 245 )
5X-RAY DIFFRACTION5chain 'A' and (resid 246 through 278 )
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 322 )
7X-RAY DIFFRACTION7chain 'A' and (resid 323 through 396 )
8X-RAY DIFFRACTION8chain 'A' and (resid 397 through 435 )
9X-RAY DIFFRACTION9chain 'A' and (resid 436 through 477 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 88 )
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 123 )
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 200 )
13X-RAY DIFFRACTION13chain 'B' and (resid 201 through 245 )
14X-RAY DIFFRACTION14chain 'B' and (resid 246 through 278 )
15X-RAY DIFFRACTION15chain 'B' and (resid 279 through 322 )
16X-RAY DIFFRACTION16chain 'B' and (resid 323 through 360 )
17X-RAY DIFFRACTION17chain 'B' and (resid 361 through 396 )
18X-RAY DIFFRACTION18chain 'B' and (resid 397 through 435 )
19X-RAY DIFFRACTION19chain 'B' and (resid 436 through 477 )
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 68 )
21X-RAY DIFFRACTION21chain 'C' and (resid 69 through 101 )
22X-RAY DIFFRACTION22chain 'C' and (resid 102 through 123 )
23X-RAY DIFFRACTION23chain 'C' and (resid 124 through 185 )
24X-RAY DIFFRACTION24chain 'C' and (resid 186 through 226 )
25X-RAY DIFFRACTION25chain 'C' and (resid 227 through 278 )
26X-RAY DIFFRACTION26chain 'C' and (resid 279 through 322 )
27X-RAY DIFFRACTION27chain 'C' and (resid 323 through 360 )
28X-RAY DIFFRACTION28chain 'C' and (resid 361 through 396 )
29X-RAY DIFFRACTION29chain 'C' and (resid 397 through 434 )
30X-RAY DIFFRACTION30chain 'C' and (resid 435 through 477 )
31X-RAY DIFFRACTION31chain 'D' and (resid 1 through 81 )
32X-RAY DIFFRACTION32chain 'D' and (resid 82 through 123 )
33X-RAY DIFFRACTION33chain 'D' and (resid 124 through 200 )
34X-RAY DIFFRACTION34chain 'D' and (resid 201 through 245 )
35X-RAY DIFFRACTION35chain 'D' and (resid 246 through 278 )
36X-RAY DIFFRACTION36chain 'D' and (resid 279 through 322 )
37X-RAY DIFFRACTION37chain 'D' and (resid 323 through 360 )
38X-RAY DIFFRACTION38chain 'D' and (resid 361 through 405 )
39X-RAY DIFFRACTION39chain 'D' and (resid 406 through 435 )
40X-RAY DIFFRACTION40chain 'D' and (resid 436 through 477 )

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