[English] 日本語
Yorodumi
- PDB-5ns8: Crystal structure of beta-glucosidase BglM-G1 mutant H75R from ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ns8
TitleCrystal structure of beta-glucosidase BglM-G1 mutant H75R from marine metagenome in complex with inhibitor 1-Deoxynojirimycin
Componentsbeta-glucosidase M - G1
KeywordsHYDROLASE / beta-glucosidase / metagenomes
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 1-DEOXYNOJIRIMYCIN
Function and homology information
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsMhaindarkar, D.C. / Gasper, R. / Lupilova, N. / Leichert, L.I. / Hofmann, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council281384 Germany
CitationJournal: Commun Biol / Year: 2018
Title: Loss of a conserved salt bridge in bacterial glycosyl hydrolase BgIM-G1 improves substrate binding in temperate environments.
Authors: Mhaindarkar, D. / Gasper, R. / Lupilov, N. / Hofmann, E. / Leichert, L.I.
History
DepositionApr 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: beta-glucosidase M - G1
B: beta-glucosidase M - G1
C: beta-glucosidase M - G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,79925
Polymers155,5323
Non-polymers2,26722
Water13,457747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-85 kcal/mol
Surface area45400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.750, 137.750, 97.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 23 or resid 25...
21(chain B and (resid 0 through 23 or resid 25...
31(chain C and (resid 0 through 23 or resid 25...

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
11HISHISALAALA(chain A and (resid 0 through 23 or resid 25...AA0 - 2315 - 38
12GLNGLNMETMET(chain A and (resid 0 through 23 or resid 25...AA25 - 9640 - 111
13PHEPHEVALVAL(chain A and (resid 0 through 23 or resid 25...AA98 - 177113 - 192
14ALAALAILEILE(chain A and (resid 0 through 23 or resid 25...AA179 - 206194 - 221
15GLUGLUSERSER(chain A and (resid 0 through 23 or resid 25...AA208 - 211223 - 226
16LEULEUASNASN(chain A and (resid 0 through 23 or resid 25...AA213 - 220228 - 235
17THRTHRALAALA(chain A and (resid 0 through 23 or resid 25...AA222 - 378237 - 393
18PHEPHESERSER(chain A and (resid 0 through 23 or resid 25...AA380 - 439395 - 454
21HISHISALAALA(chain B and (resid 0 through 23 or resid 25...BB0 - 2315 - 38
22GLNGLNMETMET(chain B and (resid 0 through 23 or resid 25...BB25 - 9640 - 111
23PHEPHEVALVAL(chain B and (resid 0 through 23 or resid 25...BB98 - 177113 - 192
24ALAALAILEILE(chain B and (resid 0 through 23 or resid 25...BB179 - 206194 - 221
25GLUGLUSERSER(chain B and (resid 0 through 23 or resid 25...BB208 - 211223 - 226
26LEULEUASNASN(chain B and (resid 0 through 23 or resid 25...BB213 - 220228 - 235
27THRTHRALAALA(chain B and (resid 0 through 23 or resid 25...BB222 - 378237 - 393
28PHEPHESERSER(chain B and (resid 0 through 23 or resid 25...BB380 - 439395 - 454
31HISHISALAALA(chain C and (resid 0 through 23 or resid 25...CC0 - 2315 - 38
32GLNGLNMETMET(chain C and (resid 0 through 23 or resid 25...CC25 - 9640 - 111
33PHEPHEVALVAL(chain C and (resid 0 through 23 or resid 25...CC98 - 177113 - 192
34ALAALAILEILE(chain C and (resid 0 through 23 or resid 25...CC179 - 206194 - 221
35GLUGLUSERSER(chain C and (resid 0 through 23 or resid 25...CC208 - 211223 - 226
36LEULEUASNASN(chain C and (resid 0 through 23 or resid 25...CC213 - 220228 - 235
37THRTHRALAALA(chain C and (resid 0 through 23 or resid 25...CC222 - 378237 - 393
38PHEPHESERSER(chain C and (resid 0 through 23 or resid 25...CC380 - 439395 - 454

-
Components

#1: Protein beta-glucosidase M - G1


Mass: 51844.121 Da / Num. of mol.: 3 / Mutation: H75R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) marine metagenome (others) / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: beta-glucosidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE / 1-Deoxynojirimycin


Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 747 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7 / Details: 0.1M Na-HEPES, 2M AmmSO4, 2% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.55→48.702 Å / Num. obs: 263967 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.672 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.16 / Χ2: 0.994 / Net I/σ(I): 11.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.5913.0372.3340.8194100.3942.429100
1.59-1.6312.9931.9241.04189660.4922.003100
1.63-1.6812.6611.6111.28185030.5681.678100
1.68-1.7313.1451.291.72179000.6921.342100
1.73-1.7913.8630.9912.44173850.8041.029100
1.79-1.8513.8690.7533.33168330.8830.782100
1.85-1.9213.7350.5864.35162440.9260.609100
1.92-213.3890.4325.92156190.9580.449100
2-2.0913.7760.3397.73149570.9740.352100
2.09-2.1914.4140.25810.38143590.9850.268100
2.19-2.3114.2820.21712.25136220.990.225100
2.31-2.4513.8680.17714.71129390.9920.184100
2.45-2.6213.6590.14617.42120950.9950.152100
2.62-2.8314.4650.12121.47113430.9960.126100
2.83-3.114.5550.09726.64103890.9980.1100
3.1-3.4713.9030.06934.8394520.9990.072100
3.47-413.5120.05342.6683450.9990.055100
4-4.914.6610.04749.8770540.9990.049100
4.9-6.9313.690.0545.6554890.9990.052100
6.93-48.70214.0570.03954.9430630.9990.04199.7

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2621refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementResolution: 1.55→48.702 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.06
RfactorNum. reflection% reflection
Rfree0.1722 13201 5 %
Rwork0.1607 --
obs0.1613 263952 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.82 Å2 / Biso mean: 27.3388 Å2 / Biso min: 12.94 Å2
Refinement stepCycle: final / Resolution: 1.55→48.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10614 0 266 747 11627
Biso mean--43.66 29.14 -
Num. residues----1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511194
X-RAY DIFFRACTIONf_angle_d0.78215206
X-RAY DIFFRACTIONf_chiral_restr0.0491530
X-RAY DIFFRACTIONf_plane_restr0.0051946
X-RAY DIFFRACTIONf_dihedral_angle_d10.9756484
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8085X-RAY DIFFRACTION8.305TORSIONAL
12B8085X-RAY DIFFRACTION8.305TORSIONAL
13C8085X-RAY DIFFRACTION8.305TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.55-1.56760.28574400.291382918731
1.5676-1.58610.30364400.289383388778
1.5861-1.60540.29124420.272983478789
1.6054-1.62570.26314360.265683018737
1.6257-1.64710.27154330.257883128745
1.6471-1.66970.26454370.261983358772
1.6697-1.69350.27144430.254883518794
1.6935-1.71880.24754370.241583388775
1.7188-1.74570.22514400.220283528792
1.7457-1.77430.21394390.206482928731
1.7743-1.80490.2194370.190583758812
1.8049-1.83770.20994400.180683458785
1.8377-1.87310.18144410.1783208761
1.8731-1.91130.18824350.165183408775
1.9113-1.95290.18184350.161883018736
1.9529-1.99830.16464470.154883948841
1.9983-2.04830.1684380.154683128750
2.0483-2.10370.16294350.153383578792
2.1037-2.16560.15244410.136783628803
2.1656-2.23550.14724430.136783478790
2.2355-2.31530.15064380.137383748812
2.3153-2.4080.14544430.137183608803
2.408-2.51760.1514370.137983808817
2.5176-2.65040.15354400.142283598799
2.6504-2.81640.16494450.14883998844
2.8164-3.03380.16274380.156683588796
3.0338-3.33910.17754410.158183908831
3.3391-3.82210.14734440.145684358879
3.8221-4.81470.1394450.129784298874
4.8147-48.7260.1764510.164685579008
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)
10.6085-0.11990.19531.6622-0.1481.08440.0487-0.0298-0.2799-0.0102-0.041-0.21740.15590.0833-0.00720.16780.00830.03680.16660.01830.3016-13.174835.15932.6028
21.2692-0.08750.32061.5117-0.59881.30350.0625-0.1363-0.11670.0663-0.0345-0.21030.07490.0521-0.02270.13890.00640.00210.13970.03310.2246-11.966241.04610.42
30.98550.09310.14792.00280.38010.4410.0322-0.1051-0.38680.0033-0.0148-0.12410.1656-0.0185-0.01460.2029-0.00690.00970.15740.05450.3013-23.17127.49827.637
41.67670.3096-0.2631.272-0.03971.084-0.07120.1331-0.4537-0.21720.0631-0.00280.259-0.1376-0.00430.2407-0.03210.00920.144-0.02710.3321-30.790324.3981-7.0624
51.03931.32120.52644.06470.71190.3109-0.11080.3328-0.5288-0.37330.158-0.30080.31510.0283-0.06460.4318-0.01160.09850.265-0.13830.4426-17.690823.3679-19.5449
66.05170.923-2.42022.2588-1.01954.6548-0.06330.3823-0.1887-0.22240.11330.05920.1378-0.4722-0.03830.1946-0.01650.02130.1229-0.00560.204-31.789736.8419-10.7195
71.8873-0.01230.34170.9231-0.27360.6106-0.07560.1613-0.1235-0.12730.0103-0.20620.1210.10590.0650.19560.00460.06550.1627-0.01830.2359-13.464741.5673-10.7734
82.8187-1.66082.28163.7189-2.41884.0333-0.02020.15010.0248-0.0903-0.0428-0.17430.05630.18040.06750.1636-0.01250.04810.1576-0.00810.2385-8.682949.5103-7.1546
90.9943-0.1455-0.41541.0040.23421.07-0.0582-0.12330.03440.11660.0299-0.0417-0.05230.01570.05810.13470.0097-0.00990.16240.01950.1161-33.030675.702517.6768
100.9944-0.3047-0.21711.0010.34581.0687-0.0361-0.0810.10320.0341-0.036-0.1244-0.10930.13380.05870.1624-0.0147-0.02730.19370.0090.1694-24.119679.099515.615
111.1811-0.2449-0.21120.48390.08770.7571-0.0451-0.07290.11160.07120.0307-0.0057-0.1062-0.02470.0030.17420.0119-0.01260.15040.00220.142-40.074686.513.4346
122.19240.6855-0.49741.8879-0.84121.2887-0.05410.0304-0.095-0.04490.08330.2065-0.0095-0.1473-0.04220.13080.0138-0.00960.16170.00890.13-55.168776.56648.3778
130.6968-0.0947-0.09461.9881-0.44710.7684-0.0531-0.00210.03040.03440.04260.1214-0.0943-0.08760.00970.11150.0121-0.02090.16010.01160.1095-51.350780.25598.6295
140.6687-0.2450.42042.6633-0.91260.7252-0.0789-0.03680.01130.2220.09270.1571-0.0195-0.0622-0.00180.1721-0.00710.03920.2020.02030.1727-55.531564.057519.7552
153.3529-0.47940.72816.449-2.80594.7397-0.11070.1455-0.0361-0.27440.16920.27840.0702-0.1845-0.05610.11220.00750.02380.1223-0.01430.0728-47.376669.46990.8716
160.5580.06540.14060.57930.25641.7792-0.0092-0.0836-0.06280.0739-0.0027-0.01840.1110.03810.00250.12130.00910.01790.15350.02880.1364-35.945961.669913.7778
171.72040.50030.65243.33712.93765.5650.0348-0.0188-0.18850.07460.0115-0.09290.22150.1113-0.05920.09730.02590.02040.1490.04270.1597-26.280959.540713.6421
180.7204-0.098-0.47931.0189-0.52550.95-0.05220.10980.0812-0.08930.0555-0.0262-0.04990.0332-0.00820.15880.00150.00420.17740.00150.1155-4.97375.6908-20.7185
190.80520.0184-0.38790.6617-0.05490.7798-0.0408-0.0114-0.04560.06150.0063-0.07720.03650.10890.04770.1510.00690.01020.20810.01360.15790.398369.768-14.9172
200.6490.1394-0.09260.5548-0.21340.9891-0.05490.1471-0.0282-0.1240.0433-0.01130.01170.04120.02270.1687-0.00970.03090.21840.00080.1362-2.982769.3686-32.4492
211.4588-1.23340.51782.7585-0.66411.26690.00040.2228-0.0379-0.25480.00140.198-0.0628-0.2286-0.00740.1718-0.0213-0.00990.27160.01370.1267-19.602274.02-39.808
221.2986-0.5405-0.52771.04860.42350.791-0.00240.28060.0189-0.1505-0.0060.0118-0.015-0.12170.0030.1641-0.0258-0.01060.23870.01650.099-15.050571.4462-38.6407
230.8278-0.4261-0.40721.26881.03831.06280.08420.21440.1697-0.2014-0.0624-0.0437-0.21850.0252-0.03340.20530.0374-0.00190.26430.06580.1937-22.247889.5138-33.4258
242.9246-1.3302-0.21816.36122.77373.9877-0.00590.3194-0.1673-0.3178-0.09970.3843-0.0827-0.26730.09970.1243-0.04350.02290.21310.01820.11-25.06668.6849-29.501
251.51980.7128-0.03490.90760.10090.78450.02310.01420.12430.0074-0.02150.0605-0.0563-0.06160.0120.15480.01060.01560.1710.01850.1476-18.308879.7862-15.6149
267.07682.9283-1.61492.5733-0.73781.80320.0745-0.15980.05430.1227-0.05320.0716-0.0133-0.0632-0.01510.16380.01280.01520.16640.00980.1186-15.439777.7696-6.3319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 46 )A2 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 108 )A47 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 209 )A109 - 209
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 298 )A210 - 298
5X-RAY DIFFRACTION5chain 'A' and (resid 299 through 325 )A299 - 325
6X-RAY DIFFRACTION6chain 'A' and (resid 326 through 349 )A326 - 349
7X-RAY DIFFRACTION7chain 'A' and (resid 350 through 416 )A350 - 416
8X-RAY DIFFRACTION8chain 'A' and (resid 417 through 440 )A417 - 440
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 46 )B2 - 46
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 108 )B47 - 108
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 209 )B109 - 209
12X-RAY DIFFRACTION12chain 'B' and (resid 210 through 265 )B210 - 265
13X-RAY DIFFRACTION13chain 'B' and (resid 266 through 298 )B266 - 298
14X-RAY DIFFRACTION14chain 'B' and (resid 299 through 325 )B299 - 325
15X-RAY DIFFRACTION15chain 'B' and (resid 326 through 349 )B326 - 349
16X-RAY DIFFRACTION16chain 'B' and (resid 350 through 416 )B350 - 416
17X-RAY DIFFRACTION17chain 'B' and (resid 417 through 440 )B417 - 440
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 46 )C2 - 46
19X-RAY DIFFRACTION19chain 'C' and (resid 47 through 108 )C47 - 108
20X-RAY DIFFRACTION20chain 'C' and (resid 109 through 209 )C109 - 209
21X-RAY DIFFRACTION21chain 'C' and (resid 210 through 265 )C210 - 265
22X-RAY DIFFRACTION22chain 'C' and (resid 266 through 298 )C266 - 298
23X-RAY DIFFRACTION23chain 'C' and (resid 299 through 325 )C299 - 325
24X-RAY DIFFRACTION24chain 'C' and (resid 326 through 349 )C326 - 349
25X-RAY DIFFRACTION25chain 'C' and (resid 350 through 416 )C350 - 416
26X-RAY DIFFRACTION26chain 'C' and (resid 417 through 440 )C417 - 440

+
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://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