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- PDB-7dwc: Bacteroides thetaiotaomicron VPI5482 BTAxe1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7dwc
TitleBacteroides thetaiotaomicron VPI5482 BTAxe1
ComponentsXylanase
KeywordsHYDROLASE / Bacteroides thetaiotaomicron VPI5482 / acetyl xylan esterase / gut bacteria-derived
Function / homologyhydrolase activity, acting on glycosyl bonds / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / xylan catabolic process / serine-type peptidase activity / Alpha/Beta hydrolase fold / Xylanase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsWang, L.Y. / Wang, Y.L. / Xin, F.J. / Sun, L.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31801475 China
National Natural Science Foundation of China (NSFC)31700701 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Rational Design for Broadened Substrate Specificity and Enhanced Activity of a Novel Acetyl Xylan Esterase from Bacteroides thetaiotaomicron.
Authors: Wang, L. / Han, X. / Wang, Y. / Wei, X. / Liu, S. / Shao, S. / Yang, S. / Sun, L. / Xin, F.
History
DepositionJan 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylanase
B: Xylanase
C: Xylanase
D: Xylanase


Theoretical massNumber of molelcules
Total (without water)117,8874
Polymers117,8874
Non-polymers00
Water10,305572
1
A: Xylanase


Theoretical massNumber of molelcules
Total (without water)29,4721
Polymers29,4721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Xylanase


Theoretical massNumber of molelcules
Total (without water)29,4721
Polymers29,4721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Xylanase


Theoretical massNumber of molelcules
Total (without water)29,4721
Polymers29,4721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Xylanase


Theoretical massNumber of molelcules
Total (without water)29,4721
Polymers29,4721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.796, 82.580, 81.534
Angle α, β, γ (deg.)90.000, 110.170, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 or (resid 2 through 3...
21(chain B and (resid 1 or (resid 2 through 3...
31(chain C and (resid 1 through 2 or (resid 3...
41(chain D and (resid 1 through 26 or (resid 27...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain A and (resid 1 or (resid 2 through 3...AA13
12LYSLYSLYSLYS(chain A and (resid 1 or (resid 2 through 3...AA2 - 34 - 5
13SERSERLEULEU(chain A and (resid 1 or (resid 2 through 3...AA-1 - 2621 - 264
14SERSERLEULEU(chain A and (resid 1 or (resid 2 through 3...AA-1 - 2621 - 264
15SERSERLEULEU(chain A and (resid 1 or (resid 2 through 3...AA-1 - 2621 - 264
16SERSERLEULEU(chain A and (resid 1 or (resid 2 through 3...AA-1 - 2621 - 264
21METMETMETMET(chain B and (resid 1 or (resid 2 through 3...BB13
22LYSLYSLYSLYS(chain B and (resid 1 or (resid 2 through 3...BB2 - 34 - 5
23SERSERLEULEU(chain B and (resid 1 or (resid 2 through 3...BB-1 - 2621 - 264
24SERSERLEULEU(chain B and (resid 1 or (resid 2 through 3...BB-1 - 2621 - 264
25SERSERLEULEU(chain B and (resid 1 or (resid 2 through 3...BB-1 - 2621 - 264
31METMETLYSLYS(chain C and (resid 1 through 2 or (resid 3...CC1 - 23 - 4
32LYSLYSLYSLYS(chain C and (resid 1 through 2 or (resid 3...CC35
33SERSERLEULEU(chain C and (resid 1 through 2 or (resid 3...CC-1 - 2621 - 264
34SERSERLEULEU(chain C and (resid 1 through 2 or (resid 3...CC-1 - 2621 - 264
35SERSERLEULEU(chain C and (resid 1 through 2 or (resid 3...CC-1 - 2621 - 264
41METMETALAALA(chain D and (resid 1 through 26 or (resid 27...DD1 - 263 - 28
42GLUGLUGLUGLU(chain D and (resid 1 through 26 or (resid 27...DD2729
43HISHISLEULEU(chain D and (resid 1 through 26 or (resid 27...DD0 - 2622 - 264
44HISHISLEULEU(chain D and (resid 1 through 26 or (resid 27...DD0 - 2622 - 264
45HISHISLEULEU(chain D and (resid 1 through 26 or (resid 27...DD0 - 2622 - 264
46HISHISLEULEU(chain D and (resid 1 through 26 or (resid 27...DD0 - 2622 - 264

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Components

#1: Protein
Xylanase


Mass: 29471.631 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Gene: BT_1008 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A909
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.1M NaCl, 0.1M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 83576 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Χ2: 0.933 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.935.70.57435790.8840.2550.630.68699.6
1.93-1.975.90.45235130.940.20.4950.54899.8
1.97-2.015.90.435380.9440.1770.4390.561100
2.01-2.055.90.3636010.9640.160.3950.591100
2.05-2.095.90.35635310.9590.1590.3910.76899.9
2.09-2.145.70.27935690.9710.1280.3080.648100
2.14-2.1960.24435710.9860.1080.2680.68100
2.19-2.256.60.24935830.9840.1050.2710.878100
2.25-2.326.60.19235460.9910.080.2080.803100
2.32-2.396.60.18835860.9890.0790.2040.843100
2.39-2.486.60.17335660.9870.0730.1880.864100
2.48-2.586.50.15635630.9910.0660.1690.973100
2.58-2.76.20.14535950.9870.0640.1581.135100
2.7-2.846.10.11935620.9940.0530.1311.149100
2.84-3.026.80.10935860.9930.0450.1191.227100
3.02-3.256.80.09635890.9950.040.1051.409100
3.25-3.586.60.08536020.9960.0360.0931.32799.9
3.58-4.0960.07736150.9960.0340.0841.218100
4.09-5.166.70.06735950.9980.0280.0731.054100
5.16-5060.06236670.9970.0280.0681.04399.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6a6o
Resolution: 1.804→28.067 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 3976 4.76 %
Rwork0.1745 79600 -
obs0.1761 83576 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.18 Å2 / Biso mean: 38.7626 Å2 / Biso min: 16.32 Å2
Refinement stepCycle: final / Resolution: 1.804→28.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8173 0 0 572 8745
Biso mean---42.96 -
Num. residues----1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078373
X-RAY DIFFRACTIONf_angle_d0.89111380
X-RAY DIFFRACTIONf_chiral_restr0.0621250
X-RAY DIFFRACTIONf_plane_restr0.0071467
X-RAY DIFFRACTIONf_dihedral_angle_d16.4594942
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4868X-RAY DIFFRACTION8.864TORSIONAL
12B4868X-RAY DIFFRACTION8.864TORSIONAL
13C4868X-RAY DIFFRACTION8.864TORSIONAL
14D4868X-RAY DIFFRACTION8.864TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.804-1.82560.32861250.3018224880
1.8256-1.84870.33621520.3011283598
1.8487-1.8730.28321290.2905281699
1.873-1.89870.32221310.2727289699
1.8987-1.92580.3071090.2643282399
1.9258-1.95450.27181480.24612855100
1.9545-1.9850.30891350.23352882100
1.985-2.01760.24141380.22912846100
2.0176-2.05240.26241450.22462871100
2.0524-2.08970.28311410.21542860100
2.0897-2.12990.24711600.1992856100
2.1299-2.17330.24391530.19512847100
2.1733-2.22050.21961580.1886280399
2.2205-2.27220.21191430.17872854100
2.2722-2.3290.22171580.1724285799
2.329-2.39190.2291510.1742845100
2.3919-2.46230.20561270.1842894100
2.4623-2.54170.21961360.17922850100
2.5417-2.63250.24151600.1862877100
2.6325-2.73780.2281470.18452857100
2.7378-2.86230.2031340.1842877100
2.8623-3.0130.20821490.17942865100
3.013-3.20150.2381150.17192917100
3.2015-3.44830.18061320.15562890100
3.4483-3.79460.15551610.14722861100
3.7946-4.34190.14431630.12982899100
4.3419-5.46370.18341320.1307289899
5.4637-28.0670.18871440.1627292199
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)
11.4457-1.2504-0.92762.5017-0.11511.2017-0.1581-0.463-0.25070.14730.1938-0.44120.09860.20790.03190.38780.0109-0.15780.62410.05080.47385.767510.890737.6821
22.05660.05720.96811.8667-0.90282.34860.0894-0.2671-0.24220.2661-0.0324-0.22530.10220.0086-0.08680.2733-0.0099-0.06090.35390.02350.2582-3.517114.860532.7938
33.8438-1.6317-0.72253.39970.05843.3508-0.0545-0.15520.05410.28390.014-0.6564-0.37030.8120.08350.2504-0.0966-0.0620.58340.01890.31835.876523.77328.5381
42.14760.31390.361.9144-0.50272.5686-0.0202-0.0470.0760.0865-0.0096-0.2296-0.20460.2357-0.00530.2043-0.00030.01690.2397-0.01350.2246-5.933923.98824.1743
51.9703-0.49050.09392.40670.50192.08270.03270.20740.2430.0019-0.0153-0.1589-0.40470.09290.00770.2572-0.02310.01980.28290.01640.2369-9.180927.114621.9675
62.20890.20710.50291.8580.6492.8510.005-0.01840.12450.0362-0.011-0.0341-0.2838-0.17610.00690.23120.0149-0.00570.26250.00950.1987-15.273724.68521.1523
75.85821.0872-0.86313.59560.00196.715-0.00630.4429-0.5527-0.46780.1446-0.36970.84340.3376-0.08420.3490.0807-0.04750.2915-0.05170.3278-7.99588.585815.2253
82.4882-1.2272-0.57452.0721-0.62062.16040.0613-0.4523-0.24440.3311-0.1027-0.18150.1607-0.11250.15930.26720.0005-0.06990.59390.06820.338218.38789.97640.7755
92.2060.6429-0.13682.96580.28823.48640.2926-0.7823-0.18430.5305-0.29210.03710.3082-0.3966-0.01940.3288-0.0673-0.03780.74920.07170.292411.037312.65272.7121
103.5718-0.3141-0.84541.51050.72023.75020.1523-0.2269-0.3717-0.01870.0597-0.0790.57970.1173-0.04590.27580.016-0.03810.44080.01930.301316.828610.0383-12.2364
111.35770.10940.32721.9509-0.08191.2805-0.0378-0.51130.03450.24980.0084-0.01660.0691-0.31560.02460.2093-0.0012-0.01630.4881-0.00940.23627.172416.6962-5.6097
123.5742-1.3358-0.55282.52240.46421.8245-0.0296-0.02950.011-0.07-0.0141-0.207-0.07650.3840.04470.1793-0.0211-0.01620.4530.00010.226919.988522.3031-9.1769
132.9421-0.154-0.63241.2054-0.42121.7538-0.0527-0.2603-0.04330.0217-0.0770.062-0.15610.29040.08750.20190.0024-0.02430.3802-0.01450.22788.404423.3037-13.8393
142.34020.1339-0.2731.8906-0.01851.4078-0.02370.04860.2077-0.0573-0.1265-0.0941-0.2844-0.18640.12920.25210.0184-0.03480.3933-0.01060.24345.282226.6492-16.2859
153.30070.11250.41231.26481.23423.3576-0.324-0.71920.9064-0.0913-0.14090.3384-0.8671-0.54990.2070.44430.1539-0.10480.626-0.18250.4655-0.807237.3233-8.0562
162.35510.39951.17761.56060.5081.775-0.073-0.1046-0.065-0.07220.05210.0723-0.0861-0.1650.05350.15810.02440.00320.3308-0.01670.1684-0.594220.2171-20.5614
176.14880.3856-0.33462.86990.3776.62460.17390.1081-0.4559-0.25450.0618-0.26170.70160.4031-0.17590.28750.07-0.00960.3435-0.01660.28024.97277.6248-21.7865
181.34390.2834-1.55644.4844-0.45161.82050.31450.5361-0.5692-0.31510.08110.00920.78790.096-0.290.60730.0836-0.21720.532-0.17580.5684-31.4501-3.7562-14.1878
193.645-0.80820.62972.40240.6223.37530.34050.6297-0.3524-0.32040.2464-0.3340.33240.6921-0.34160.33150.0763-0.09420.6072-0.18050.3687-26.10591.8496-16.4223
201.59831.0999-0.72013.1429-0.75112.65340.40680.0344-0.77850.49180.0216-0.1610.94860.3308-0.26620.5166-0.0264-0.2080.2969-0.00150.4454-30.8524-1.7914-0.9345
211.78230.08761.06842.39660.65931.91490.18370.3356-0.271-0.07640.0202-0.18130.12650.4907-0.22950.23130.0163-0.02060.425-0.07470.2455-25.16728.3441-9.249
221.78011.7422-0.9095.0858-2.02922.27240.05580.1848-0.1742-0.1682-0.03860.21650.168-0.3409-0.22130.2653-0.0249-0.05560.448-0.03030.2968-39.0227.8504-6.314
232.173-0.20060.13621.81230.21292.178-0.0651-0.0564-0.09980.01130.01640.0475-0.23220.00350.03530.17760.0022-0.02040.3314-0.00090.1652-29.41317.8593-1.1496
243.44920.58260.11272.88630.46584.1373-0.2850.30170.3581-0.26590.04390.1279-0.93520.17150.11630.5306-0.057-0.05460.39950.07220.2469-28.3330.2659-10.2825
251.91750.00041.22181.49180.12952.319-0.08320.00670.0406-0.03610.0747-0.0031-0.3432-0.0147-0.02830.244-0.00890.0060.32880.00110.1772-24.026220.17066.3128
263.25940.80930.34272.27640.56353.16060.21130.1898-0.27840.13130.1711-0.26510.3730.5938-0.30250.28770.0529-0.06970.438-0.08080.3246-15.69576.99234.0227
272.8259-0.1315-0.66574.6329-0.43142.66950.04380.6143-0.4915-0.78740.00580.52170.9833-0.3861-0.11290.6694-0.1291-0.10170.4643-0.12060.4836-48.0653-2.487624.4126
281.8621-0.20940.62142.13371.10452.6005-0.01750.0206-0.256-0.32110.17360.12180.404-0.1173-0.17150.3733-0.0751-0.05390.42090.00740.2896-41.23025.048429.2318
293.28391.8852-1.75943.9553-1.24642.9256-0.25650.009-0.2343-0.0403-0.06060.1850.0059-0.61930.33420.3953-0.037-0.08660.628-0.010.3925-53.75959.236532.3736
301.81690.17630.51161.94980.37612.3565-0.0978-0.06930.1539-0.2020.0760.1168-0.1868-0.16120.07430.2185-0.0047-0.02120.35660.01290.1729-38.201619.833338.0423
314.46840.7186-1.53393.2344-0.01864.9564-0.2433-0.6385-0.39430.05990.27230.02771.05-0.236-0.05720.3837-0.0165-0.04750.39410.06170.2444-35.23664.383247.6059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 24 )A-1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 97 )A25 - 97
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 119 )A98 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 138 )A120 - 138
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 164 )A139 - 164
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 247 )A165 - 247
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 262 )A248 - 262
8X-RAY DIFFRACTION8chain 'B' and (resid -1 through 24 )B-1 - 24
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 43 )B25 - 43
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 56 )B44 - 56
11X-RAY DIFFRACTION11chain 'B' and (resid 57 through 97 )B57 - 97
12X-RAY DIFFRACTION12chain 'B' and (resid 98 through 119 )B98 - 119
13X-RAY DIFFRACTION13chain 'B' and (resid 120 through 138 )B120 - 138
14X-RAY DIFFRACTION14chain 'B' and (resid 139 through 164 )B139 - 164
15X-RAY DIFFRACTION15chain 'B' and (resid 165 through 184 )B165 - 184
16X-RAY DIFFRACTION16chain 'B' and (resid 185 through 247 )B185 - 247
17X-RAY DIFFRACTION17chain 'B' and (resid 248 through 262 )B248 - 262
18X-RAY DIFFRACTION18chain 'C' and (resid -1 through 24 )C-1 - 24
19X-RAY DIFFRACTION19chain 'C' and (resid 25 through 43 )C25 - 43
20X-RAY DIFFRACTION20chain 'C' and (resid 44 through 56 )C44 - 56
21X-RAY DIFFRACTION21chain 'C' and (resid 57 through 97 )C57 - 97
22X-RAY DIFFRACTION22chain 'C' and (resid 98 through 119 )C98 - 119
23X-RAY DIFFRACTION23chain 'C' and (resid 120 through 164 )C120 - 164
24X-RAY DIFFRACTION24chain 'C' and (resid 165 through 184 )C165 - 184
25X-RAY DIFFRACTION25chain 'C' and (resid 185 through 232 )C185 - 232
26X-RAY DIFFRACTION26chain 'C' and (resid 233 through 262 )C233 - 262
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 24 )D1 - 24
28X-RAY DIFFRACTION28chain 'D' and (resid 25 through 97 )D25 - 97
29X-RAY DIFFRACTION29chain 'D' and (resid 98 through 119 )D98 - 119
30X-RAY DIFFRACTION30chain 'D' and (resid 120 through 247 )D120 - 247
31X-RAY DIFFRACTION31chain 'D' and (resid 248 through 262 )D248 - 262

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