[English] 日本語
Yorodumi
- PDB-5bt9: Crystal Structure of FolM Alternative dihydrofolate reductase 1 f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bt9
TitleCrystal Structure of FolM Alternative dihydrofolate reductase 1 from Brucella canis complexed with NADP
Components3-oxoacyl-(Acyl-carrier-protein) reductase
KeywordsOXIDOREDUCTASE / SSGCID / FolM / Alternative dihydrofolate reductase 1 / fabG / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-(Acyl-carrier-protein) reductase
Similarity search - Component
Biological speciesBrucella canis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structures of FolM alternative dihydrofolate reductase 1 from Brucella suis and Brucella canis.
Authors: Porter, I. / Neal, T. / Walker, Z. / Hayes, D. / Fowler, K. / Billups, N. / Rhoades, A. / Smith, C. / Smith, K. / Staker, B.L. / Dranow, D.M. / Mayclin, S.J. / Subramanian, S. / Edwards, T.E. ...Authors: Porter, I. / Neal, T. / Walker, Z. / Hayes, D. / Fowler, K. / Billups, N. / Rhoades, A. / Smith, C. / Smith, K. / Staker, B.L. / Dranow, D.M. / Mayclin, S.J. / Subramanian, S. / Edwards, T.E. / Myler, P.J. / Asojo, O.A.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references / Source and taxonomy
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-(Acyl-carrier-protein) reductase
B: 3-oxoacyl-(Acyl-carrier-protein) reductase
C: 3-oxoacyl-(Acyl-carrier-protein) reductase
D: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9308
Polymers119,9574
Non-polymers2,9744
Water13,043724
1
A: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7332
Polymers29,9891
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7332
Polymers29,9891
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7332
Polymers29,9891
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3-oxoacyl-(Acyl-carrier-protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7332
Polymers29,9891
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18800 Å2
ΔGint-90 kcal/mol
Surface area32450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.570, 75.600, 99.180
Angle α, β, γ (deg.)90.000, 109.230, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
3-oxoacyl-(Acyl-carrier-protein) reductase


Mass: 29989.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella canis (strain ATCC 23365 / NCTC 10854) (bacteria)
Strain: ATCC 23365 / NCTC 10854 / Gene: fabG, BCAN_A0712 / Plasmid: BrcaA.00010.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9MA73
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: BrcaA.00010.a.B1.PS02349 at 32.3 mg/ml incubated with 6 mM NADP, then mixed 1:1 with MCSG1(a1): 0.1 M HEPES:NaOH, pH=7.5, 20% PEG-8000, cryoprotected with 20% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 2, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 164992 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 15.63 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.053 / Χ2: 0.985 / Net I/σ(I): 18.26 / Num. measured all: 783894
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.544.80.8970.4933.395733612583119080.55394.6
1.54-1.580.9170.41145610712293116670.46294.9
1.58-1.630.9470.3344.855449711937113420.37595
1.63-1.680.9650.2546.185314111590110640.28595.5
1.68-1.730.9740.2117.335178611284107980.23895.7
1.73-1.790.9790.188.514995410860104190.20295.9
1.79-1.860.9890.13810.624870010565101670.15596.2
1.86-1.940.9920.10513.51467281011097600.11896.5
1.94-2.020.9950.08216.5544818969693820.09296.8
2.02-2.120.9970.06619.9642975927289910.07497
2.12-2.240.9980.05423.8141109885986210.06197.3
2.24-2.370.9980.04826.0738714834881400.05497.5
2.37-2.540.9980.04229.5136315787577030.04797.8
2.54-2.740.9980.03932.4933744732871840.04498
2.74-30.9980.03536.6331053676566490.03998.3
3-3.350.9990.03140.1927909612260260.03598.4
3.35-3.870.9990.02844.4924710542053460.03198.6
3.87-4.740.9990.02546.7820638459145030.02898.1
4.74-6.710.9990.02646.5415974356235130.02998.6
6.710.9990.02446.057686201418090.02789.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E7W

1e7w


Resolution: 1.5→36.149 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1878 8084 4.92 %
Rwork0.1686 156072 -
obs0.1695 164156 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.65 Å2 / Biso mean: 27.637 Å2 / Biso min: 8.85 Å2
Refinement stepCycle: final / Resolution: 1.5→36.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7542 0 192 726 8460
Biso mean--26.65 35.01 -
Num. residues----990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068143
X-RAY DIFFRACTIONf_angle_d1.13111178
X-RAY DIFFRACTIONf_chiral_restr0.0471273
X-RAY DIFFRACTIONf_plane_restr0.0061455
X-RAY DIFFRACTIONf_dihedral_angle_d16.6024907
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51710.28772350.24864573480885
1.5171-1.53490.27522750.2355092536794
1.5349-1.55360.25372800.23325041532195
1.5536-1.57330.23362590.22475141540095
1.5733-1.5940.262610.21485123538495
1.594-1.61580.2412830.20995132541595
1.6158-1.63890.2362610.20695127538895
1.6389-1.66340.22142560.19945149540595
1.6634-1.68940.23962480.19855132538096
1.6894-1.71710.22292820.19125147542996
1.7171-1.74670.21162620.19035200546296
1.7467-1.77840.22682860.19235167545396
1.7784-1.81260.21062770.18565171544896
1.8126-1.84960.21062760.17925208548496
1.8496-1.88980.19522590.17585209546896
1.8898-1.93380.21542720.17985207547997
1.9338-1.98220.20582810.17545222550397
1.9822-2.03580.20262630.1765233549697
2.0358-2.09570.19542620.17015216547897
2.0957-2.16330.17952590.16595293555297
2.1633-2.24060.16632730.16375275554897
2.2406-2.33030.19752650.16945286555198
2.3303-2.43630.18782630.16795320558398
2.4363-2.56470.19122650.17295298556398
2.5647-2.72540.20212580.175344560298
2.7254-2.93570.20422720.17075344561698
2.9357-3.2310.1942900.16965327561799
3.231-3.69810.16992740.15435408568299
3.6981-4.65770.12712920.12645360565298
4.6577-36.15980.16242950.1545327562296
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)
13.08761.2911-0.36122.55140.79182.61390.02340.3506-0.1762-0.04020.0694-0.25670.2068-0.0309-0.07880.09150.00150.02250.22990.0110.156362.01531.056216.2324
20.1554-0.40530.10531.5772-0.70941.8609-0.02370.83060.3221-0.17210.0871-0.2139-0.00030.08740.16560.1616-0.05520.03290.46490.13660.233662.96479.60629.1133
31.8278-0.9411.36111.9213-0.5051.1157-0.00150.77150.224-0.33170.3647-0.1464-0.0351-0.07520.10850.1898-0.03820.07530.53150.20380.196851.15356.11966.0785
40.54430.17570.47570.6216-0.31441.0208-0.0410.8320.1437-0.14610.07-0.14930.0349-0.04280.03940.1589-0.02290.02430.46280.0660.151945.47092.87769.3372
50.56870.71520.02781.1929-0.37181.549-0.01040.6110.2082-0.0870.0653-0.0962-0.1117-0.0905-0.09340.10790.00270.03010.28460.07520.165343.80355.735114.3788
60.9511.4352-0.44922.2377-0.29362.52980.10920.38360.3925-0.1288-0.0407-0.1557-0.6077-0.00310.0220.28510.02680.09890.19640.13240.369644.16424.581723.3377
71.486-0.47390.33890.7634-0.12150.713-0.00540.19750.246-0.00790.05110.0334-0.13520.0147-0.01230.12370.00140.02740.09070.04410.150246.28828.723924.7248
84.35033.67214.56615.01422.95665.2134-0.255-2.04790.1752-2.53531.50520.0692-3.6822-3.3587-1.24320.65420.2633-0.05580.65520.28160.594222.869721.609127.7108
94.8205-0.2506-0.33111.63220.77423.9595-0.0062-0.3350.02070.0730.0644-0.11460.02420.2739-0.00080.09170.0182-0.02470.14-0.01390.093452.77024.458246.7397
105.13780.82511.62492.6546-0.24392.11940.0003-0.63920.02330.4195-0.1106-0.10990.03810.30910.09960.27340.0077-0.02920.37810.02560.150449.92853.145755.6316
113.48791.36260.36462.2240.22851.44950.133-0.3994-0.0010.1359-0.0644-0.00830.0683-0.0837-0.07380.13150.00480.00790.14880.00520.079436.57113.977447.8999
121.5542-0.0122-0.11460.55320.13030.74530.0094-0.01-0.13510.01490.0132-0.03690.07490.0467-0.03020.10550.00950.00130.06340.01010.106142.1972-1.027733.6706
1322-1.92062220.1303-4.46828.7166.57512.6732-0.2154-2.6416-6.4772-2.80560.6480.09740.17960.6747-0.2060.941131.6615-22.374813.2685
140.75040.58030.56890.79020.2041.123-0.13320.58250.1826-0.31890.48870.1285-0.1704-0.13120.48230.1522-0.1195-0.16540.9806-0.12930.094410.4835-2.2728-0.293
150.7520.05650.54080.8570.50841.3875-0.1120.1944-0.003-0.28380.11410.0625-0.17470.12910.08330.4558-0.2526-0.20861.0021-0.20.21636.9561-9.6189-8.9751
160.5918-0.13930.76970.70550.07031.09470.0037-0.0589-0.0035-0.36270.2431-0.0348-0.14860.2116-0.05770.4969-0.2475-0.03741.2397-0.1360.225816.7239-1.3944-9.0113
170.8947-0.18590.16681.00560.35490.2319-0.07450.87480.0815-0.44480.1332-0.1315-0.07790.0449-0.01450.2763-0.0662-0.02570.94350.00610.138223.4662-0.8208-1.8976
180.50460.28940.12490.2032-0.01080.3318-0.10660.8641-0.044-0.14940.12330.0319-0.0559-0.00830.0050.1936-0.0280.02260.69040.01970.129926.55871.35774.2298
192.02170.1635-0.12920.47580.07440.6574-0.07051.0202-0.1743-0.13310.0480.11410.02390.0455-0.00290.1516-0.01770.0060.5227-0.03330.121525.1372-0.88099.0609
200.0863-0.3058-0.61212.11831.03665.8409-0.15490.6421-0.6754-0.0653-0.0038-0.0820.5538-0.02450.16810.23860.00060.0120.3547-0.23220.492820.2138-19.797216.7099
212.4984-0.140.25361.32890.27321.01750.03110.5972-0.2278-0.0326-0.04180.07620.0792-0.0319-0.00970.1122-0.01030.01690.2341-0.04780.120118.6614-4.743817.5238
226.09240.21560.38265.7104-1.87955.49470.00830.2762-0.3033-0.2598-0.02750.24810.2827-0.17980.0820.0599-0.00960.02220.1579-0.00860.13071.9448-3.413632.0025
233.59410.85060.70171.79140.21613.0252-0.02520.04460.25170.00490.01830.0707-0.1676-0.08420.02210.08080.02740.0170.1156-0.01630.15980.32623.327632.7293
245.42521.15441.63812.371.47753.90180.1581-0.4397-0.07940.2216-0.12530.11950.0131-0.22310.01860.1428-0.0120.03880.12410.00010.1484-1.78681.689141.0632
254.0732.77670.50474.9451-0.69332.76470.1271-0.1041-0.14110.3011-0.01470.17030.0531-0.2592-0.09930.12050.00420.02220.08460.01230.16312.9941-7.925439.0201
266.29074.26871.61664.07131.12160.5130.1016-0.35520.66480.198-0.08210.0744-0.07980.0568-0.04750.1731-0.01250.03470.1899-0.10030.334920.646414.407742.4173
273.81392.17740.82763.97941.20782.62450.0998-0.3388-0.15520.1029-0.0591-0.12450.0873-0.0124-0.01810.09320.01390.02190.13450.01420.104217.1857-1.020342.6251
282.16850.08490.03970.9178-0.14111.4944-0.02780.09560.1113-0.02020.03280.11040.0592-0.05570.02260.11220.01280.00750.05950.00040.098417.16841.870430.9466
291.7942-0.109-0.040710.09141.6511-0.00950.05080.1058-0.0750.00210.1213-0.1058-0.0524-0.01010.09450.00440.00670.0737-0.00060.118418.522.148331.3715
303.29391.7767-0.36963.3166-2.52772.3453-0.21520.1470.97550.2454-0.01190.2896-0.49450.04020.07220.2933-0.0003-0.08940.22690.12840.497113.525319.860719.8516
312.06070.6078-0.18231.07120.30011.12380.0160.42320.2562-0.0264-0.0290.0463-0.1336-0.0293-0.01960.12010.0159-0.0020.15660.05670.145616.15335.93321.1287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 77 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 108 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 157 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 199 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 217 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 253 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 254 through 254 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 7 through 46 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 77 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 78 through 133 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 134 through 255 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 256 through 256 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 6 through 46 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 47 through 60 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 61 through 74 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 75 through 108 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 109 through 157 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 158 through 199 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 200 through 217 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 218 through 255 )C0
22X-RAY DIFFRACTION22chain 'D' and (resid 8 through 22 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 23 through 46 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 47 through 77 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 78 through 94 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 95 through 108 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 109 through 133 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 134 through 157 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 158 through 202 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 203 through 217 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 218 through 256 )D0

+
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