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- PDB-3bje: Crystal structure of Trypanosoma brucei nucleoside phosphorylase ... -

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Basic information

Entry
Database: PDB / ID: 3bje
TitleCrystal structure of Trypanosoma brucei nucleoside phosphorylase shows uridine phosphorylase activity
ComponentsNucleoside phosphorylase, putativePurine nucleoside phosphorylase
KeywordsTRANSFERASE / nucleoside phosphorylase / uridine phosphorylase / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa Consortium / MSGPP / Trypanosoma / brucei / sleeping sickness / Glycosyltransferase / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


uridine phosphorylase activity / nucleoside metabolic process / purine-nucleoside phosphorylase activity / ciliary plasm / Transferases; Glycosyltransferases; Pentosyltransferases / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-O-phosphono-alpha-D-ribofuranose / URACIL / Nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.44 Å
AuthorsLarson, E.T. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The Crystal Structure and Activity of a Putative Trypanosomal Nucleoside Phosphorylase Reveal It to be a Homodimeric Uridine Phosphorylase
Authors: Larson, E.T. / Mudeppa, D.G. / Gillespie, J.R. / Mueller, N. / Napuli, A.J. / Arif, J.A. / Ross, J. / Arakaki, T.L. / Lauricella, A. / Detitta, G. / Luft, J. / Zucker, F. / Verlinde, C.L. / ...Authors: Larson, E.T. / Mudeppa, D.G. / Gillespie, J.R. / Mueller, N. / Napuli, A.J. / Arif, J.A. / Ross, J. / Arakaki, T.L. / Lauricella, A. / Detitta, G. / Luft, J. / Zucker, F. / Verlinde, C.L. / Fan, E. / Van Voorhis, W.C. / Buckner, F.S. / Rathod, P.K. / Hol, W.G. / Merritt, E.A.
History
DepositionDec 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / software / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600 HETEROGEN THE FORMATION OF A COMPLEX WITH URACIL AND RIBOSE-1-PHOSPHATE RESULTS FROM ... HETEROGEN THE FORMATION OF A COMPLEX WITH URACIL AND RIBOSE-1-PHOSPHATE RESULTS FROM COCRYSTALLIZATION WITH URIDINE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside phosphorylase, putative
B: Nucleoside phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7337
Polymers76,0082
Non-polymers7245
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.015, 95.387, 63.483
Angle α, β, γ (deg.)90.000, 105.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleoside phosphorylase, putative / Purine nucleoside phosphorylase


Mass: 38004.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: GUTat10.1 / Gene: Tb927.8.4430 / Plasmid: BG1861 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q57VZ2, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Sugar ChemComp-R1P / 1-O-phosphono-alpha-D-ribofuranose / RIBOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-ribose / 1-O-phosphono-D-ribose / 1-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-URA / URACIL / Uracil


Mass: 112.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N2O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Description: The Blu-ice software package was used for data collection. The reference is: McPhillips T.M., McPhillips S.E., Chiu H.J., Cohen A.E., Deacon A.M., Ellis P.J., Garman E., Gonzalez A., ...Description: The Blu-ice software package was used for data collection. The reference is: McPhillips T.M., McPhillips S.E., Chiu H.J., Cohen A.E., Deacon A.M., Ellis P.J., Garman E., Gonzalez A., Sauter N.K., Phizackerley R.P., Soltis S.M., Kuhn P., Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. J Synchrotron Radiat. 2002 Nov 1, 9(Pt 6):401-6. Epub 2002 Nov 1. PMID: 12409628.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 39% PEG 8000, 0.1 M Tris-HCl pH 8.5, 0.1 M Sodium phosphate monobasic, 10 mM Uridine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91724, 0.97910, 0.91160
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 28, 2007 / Details: Mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.917241
20.97911
30.91161
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 8.1 / Number: 104235 / Rmerge(I) obs: 0.109 / Χ2: 1.2 / D res high: 2.27 Å / D res low: 50 Å / Num. obs: 31735 / % possible obs: 95.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.895099.910.0712.5193.4
3.884.8910010.0651.6683.4
3.393.8810010.0791.1913.4
3.083.3910010.1131.0573.4
2.863.0810010.1690.9243.4
2.692.8610010.2230.9013.4
2.562.6996.810.240.8533.2
2.452.5691.310.2560.8523.1
2.352.4584.510.2950.8133
2.272.3577.810.30.8093
ReflectionResolution: 1.44→40 Å / Num. all: 123263 / Num. obs: 123263 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.033 / Net I/σ(I): 8.4
Reflection shellResolution: 1.44→1.5 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 1.2 / Num. unique all: 9430 / Χ2: 1.03 / % possible all: 73.4

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MADD res high: 2.3 Å / D res low: 50 Å / FOM : 0.23 / Reflection: 27846
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength10.97916.34-8.45
12 wavelength20.91163.3-1.7
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se1.9850.7290.5010.1960.48
2Se39.5590.0920.4370.4710.881
3Se39.3150.7460.540.2250.277
4Se18.2550.7730.540.1660.788
5Se20.3040.7680.5270.390.772
6Se31.6580.4070.6030.0890.833
7Se10.7630.8640.3850.1340.52
8Se10.5530.5430.4450.219
9Se5.7680.6160.6950.0910.506
10Se59.7010.8770.6190.1081.091
11Se32.5810.1550.5490.2370.642
12Se33.3240.0670.60.420.723
13Se14.5880.8160.6950.4090.604
14Se22.250.7830.5790.3910.614
15Se10.1310.5450.2940.172
16Se40.30.8540.6790.4680.636
17Se10.8310.6250.0560.151
18Se46.0160.1760.580.2750.359
19Se10.540.0040.0620.209
20Se1.9770.9330.1330.3970.219
21Se40.2980.5450.7650.2860.579
22Se10.1230.7330.4950.01
Phasing MAD shell
Resolution (Å)FOM Reflection
8.32-500.461488
5.24-8.320.442591
4.09-5.240.393328
3.47-4.090.33896
3.06-3.470.214155
2.77-3.060.144321
2.55-2.770.114208
2.37-2.550.083859
Phasing dmFOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0.7 / Reflection: 28486 / Reflection acentric: 27669 / Reflection centric: 817
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.5-38.0940.90.910.8114691337132
4.1-6.50.880.880.8244044203201
3.2-4.10.820.830.7354585282176
2.8-3.20.680.680.7251455032113
2.4-2.80.510.510.4780497905144
2.3-2.40.390.390.413961391051

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Processing

Software
NameVersionClassificationNB
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.44→35.38 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.283 / SU ML: 0.044 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 6191 5 %RANDOM
Rwork0.155 ---
all0.156 123193 --
obs0.156 123193 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å2-0.62 Å2
2---0.4 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.44→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 45 501 5530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225182
X-RAY DIFFRACTIONr_bond_other_d0.0020.023544
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9727017
X-RAY DIFFRACTIONr_angle_other_deg0.86738649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8565678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39823.425219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65115916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4681544
X-RAY DIFFRACTIONr_chiral_restr0.0720.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
X-RAY DIFFRACTIONr_nbd_refined0.2080.2989
X-RAY DIFFRACTIONr_nbd_other0.2030.23970
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22573
X-RAY DIFFRACTIONr_nbtor_other0.0830.22732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2439
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0720.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.216
X-RAY DIFFRACTIONr_mcbond_it1.72243407
X-RAY DIFFRACTIONr_mcbond_other0.47741356
X-RAY DIFFRACTIONr_mcangle_it2.26765287
X-RAY DIFFRACTIONr_scbond_it2.94862017
X-RAY DIFFRACTIONr_scangle_it4.3101718
LS refinement shellResolution: 1.44→1.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 290 -
Rwork0.268 5846 -
all-6136 -
obs-9605 63.883 %
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)
12.58670.6047-0.25841.1134-0.12020.4108-0.07510.1084-0.2521-0.131-0.02730.08930.0724-0.04550.1024-0.0140.004-0.0102-0.0105-0.03720.0166-4.434-6.659610.8574
20.68220.432-0.2290.69180.16240.36570.01410.0306-0.1278-0.0426-0.03950.07460.0361-0.02880.0254-0.02960.0131-0.00840.0077-0.0184-0.0069-1.2138-2.39410.7313
34.4763-1.9251.24687.571-0.3556.18680.01740.41910.1542-0.5543-0.08440.2672-0.0507-0.36620.06710.0380.0208-0.07110.0640.0292-0.0593-4.77845.6912-6.6783
41.64820.16070.29130.74460.06731.53150.00520.1660.1683-0.1384-0.03430.2108-0.1307-0.16890.02910.00790.0337-0.03270.03860.00150.0259-5.09478.8948.2537
51.33540.2332-0.12960.91840.15380.65690.0408-0.15260.17920.0223-0.07540.0923-0.1427-0.09030.03460.00110.01850.0050.0216-0.0405-0.00415.750413.272120.9439
62.8445-0.6930.75491.9490.66971.6294-0.050.0740.275-0.1373-0.04410.0824-0.2917-0.02850.09410.0340.0164-0.0131-0.0424-0.02270.009211.670824.221820.9647
72.87390.5985-0.14741.4181-0.11590.95160.0407-0.38390.07170.1275-0.11690.3937-0.0579-0.25230.0762-0.04560.03490.03310.0672-0.07670.0555-8.156511.606724.8451
81.6993-0.19060.32660.96510.17950.6898-0.0228-0.19570.02820.1411-0.03380.0432-0.0005-0.13860.05660.00780.00090.02540.019-0.0224-0.042812.62146.972930.7767
90.7080.28820.50.69340.15950.8849-0.0155-0.14530.1780.0441-0.07890.0999-0.1088-0.19260.0945-0.03180.03690.0094-0.0003-0.0438-0.02075.042414.279923.672
1012.44368.04880.36835.84772.08575.33070.6567-1.4337-0.08490.9377-0.5407-0.1983-0.2822-0.5124-0.11590.03550.018-0.0050.06950.02050.03626.64315.159539.5171
113.74540.09161.7572.887-1.8625.08590.1524-0.4806-0.21860.1539-0.11640.06040.2709-0.3437-0.036-0.0552-0.04170.03150.0848-0.02730.0124-9.61060.179127.8814
1210.989928.934-8.6452108.7779-15.71198.32490.3821-0.52120.54831.6311-0.16173.1784-0.1214-0.1901-0.22040.01840.0294-0.00010.07260.03030.010213.3018-6.004538.5821
130.6507-0.29960.0970.9948-0.07180.47250.0119-0.0533-0.09490.0336-0.01330.12980.0534-0.05070.0014-0.0091-0.00920.0134-0.02170.0169-0.018118.8964-14.577124.5608
1416.686-3.07958.635516.91233.33747.38360.1789-2.3522-0.62711.64470.19970.67610.7907-1.0418-0.37860.0472-0.05290.0380.11850.0863-0.155326.0607-6.92142.7261
150.5091-0.09010.14860.90820.34341.16330.0368-0.06490.03020.15030.0293-0.14010.11410.1676-0.0661-0.0082-0.01030.00270.0072-0.0049-0.009532.2294-6.63227.9533
160.6794-0.3241-0.31321.33770.05450.92510.03860.05080.043-0.1315-0.0245-0.1369-0.01640.0948-0.01410.0194-0.00110.01770.02750.01050.007527.36331.541811.7307
172.4576-0.38541.28511.1996-1.27134.9405-0.0883-0.06330.15390.0058-0.0253-0.1794-0.40070.15840.1135-0.0143-0.02740.0192-0.00020.0490.011934.407511.14498.2423
180.6482-0.29650.03841.37540.09550.40660.02360.082-0.0204-0.1333-0.0231-0.14280.03160.0376-0.00050.00860.0020.03440.0026-0.0016-0.009632.047-6.06219.7072
191.1026-0.47910.04671.2166-0.1150.4030.06250.1638-0.0678-0.1928-0.0560.01690.07540.0162-0.00660.03610.01530.01220.0104-0.0077-0.042519.2983-3.21852.236
201.4435-0.23640.04841.1103-0.11320.84220.04860.22290.0737-0.1096-0.0939-0.13460.00950.10210.04530.01390.00650.0310.02070.025-0.041825.95525.96110.891
210.8199-0.20060.22861.2072-0.10850.80450.01940.07260.0101-0.1233-0.02720.01510.0189-0.03440.00780.01350.00540.01440.00720.0011-0.007125.132-3.595112.9354
222.9099-0.37942.53163.3372-0.80774.93660.00180.1799-0.0403-0.53850.02410.35230.1224-0.2202-0.0260.0589-0.0013-0.02480.0028-0.0062-0.004522.3793-16.93364.9594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 6323 - 71
2X-RAY DIFFRACTION2AA64 - 10672 - 114
3X-RAY DIFFRACTION3AA107 - 118115 - 126
4X-RAY DIFFRACTION4AA119 - 145127 - 153
5X-RAY DIFFRACTION5AA146 - 174154 - 182
6X-RAY DIFFRACTION6AA175 - 196183 - 204
7X-RAY DIFFRACTION7AA197 - 227205 - 235
8X-RAY DIFFRACTION8AA228 - 257236 - 265
9X-RAY DIFFRACTION9AA258 - 309266 - 317
10X-RAY DIFFRACTION10AA310 - 319318 - 327
11X-RAY DIFFRACTION11AA320 - 341328 - 349
12X-RAY DIFFRACTION12BB15 - 2123 - 29
13X-RAY DIFFRACTION13BB22 - 10530 - 113
14X-RAY DIFFRACTION14BB106 - 113114 - 121
15X-RAY DIFFRACTION15BB114 - 145122 - 153
16X-RAY DIFFRACTION16BB146 - 175154 - 183
17X-RAY DIFFRACTION17BB176 - 191184 - 199
18X-RAY DIFFRACTION18BB192 - 224200 - 232
19X-RAY DIFFRACTION19BB225 - 253233 - 261
20X-RAY DIFFRACTION20BB254 - 283262 - 291
21X-RAY DIFFRACTION21BB284 - 313292 - 321
22X-RAY DIFFRACTION22BB314 - 341322 - 349

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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

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