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- PDB-8oic: Trichomonas vaginalis riboside hydrolase (His-tagged) -

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Basic information

Entry
Database: PDB / ID: 8oic
TitleTrichomonas vaginalis riboside hydrolase (His-tagged)
ComponentsInosine-uridine preferring nucleoside hydrolase family protein
KeywordsHYDROLASE / NH-fold / nucleoside hydrolase / riboside hydrolase / nicotinamide riboside
Function / homologypurine nucleosidase activity / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / purine nucleoside catabolic process / cytosol / Inosine-uridine preferring nucleoside hydrolase family protein
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPatrone, M. / Stockman, B.J. / Degano, M.
Funding support Italy, United States, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG25764 Italy
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI128585 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: A riboside hydrolase that salvages both nucleobases and nicotinamide in the auxotrophic parasite Trichomonas vaginalis.
Authors: Patrone, M. / Galasyn, G.S. / Kerin, F. / Nyitray, M.M. / Parkin, D.W. / Stockman, B.J. / Degano, M.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-uridine preferring nucleoside hydrolase family protein
B: Inosine-uridine preferring nucleoside hydrolase family protein
C: Inosine-uridine preferring nucleoside hydrolase family protein
D: Inosine-uridine preferring nucleoside hydrolase family protein
E: Inosine-uridine preferring nucleoside hydrolase family protein
F: Inosine-uridine preferring nucleoside hydrolase family protein
G: Inosine-uridine preferring nucleoside hydrolase family protein
H: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,65324
Polymers331,0278
Non-polymers1,62616
Water4,288238
1
A: Inosine-uridine preferring nucleoside hydrolase family protein
B: Inosine-uridine preferring nucleoside hydrolase family protein
C: Inosine-uridine preferring nucleoside hydrolase family protein
D: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,32612
Polymers165,5134
Non-polymers8138
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Inosine-uridine preferring nucleoside hydrolase family protein
F: Inosine-uridine preferring nucleoside hydrolase family protein
G: Inosine-uridine preferring nucleoside hydrolase family protein
H: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,32612
Polymers165,5134
Non-polymers8138
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.055, 94.665, 120.589
Angle α, β, γ (deg.)105.081, 89.959, 93.826
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A
137A
147A
158A
168A
179A
189A
1910A
2010A
2111A
2211A
2312A
2412A
2513A
2613A
2714A
2814A
2915A
3015A
3116A
3216A
3317A
3417A
3518A
3618A
3719A
3819A
3920A
4020A
4121A
4221A
4322A
4422A
4523A
4623A
4724A
4824A
4925A
5025A
5126A
5226A
5327A
5427A
5528A
5628A

NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 346 / Label seq-ID: 21 - 366

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266
1377
1477
1588
1688
1799
1899
191010
201010
211111
221111
231212
241212
251313
261313
271414
281414
291515
301515
311616
321616
331717
341717
351818
361818
371919
381919
392020
402020
412121
422121
432222
442222
452323
462323
472424
482424
492525
502525
512626
522626
532727
542727
552828
562828

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

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Components

#1: Protein
Inosine-uridine preferring nucleoside hydrolase family protein


Mass: 41378.324 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_092730 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2FTT0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M bicine pH 8.5, 20% (w/v) PEG 5000 monomethyl ether, 3% sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.578→116.42 Å / Num. obs: 96699 / % possible obs: 98.5 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rpim(I) all: 0.089 / Rsym value: 0.147 / Net I/σ(I): 6.3
Reflection shellResolution: 2.578→2.623 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4868 / CC1/2: 0.361 / Rpim(I) all: 0.855 / Rsym value: 1.432 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→116.418 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.201 / SU B: 38.785 / SU ML: 0.339 / Average fsc free: 0.9507 / Average fsc work: 0.9667 / Cross valid method: THROUGHOUT / ESU R Free: 0.395
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 3857 5.107 %Random
Rwork0.2093 71660 --
all0.211 ---
obs-75517 98.572 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 64.186 Å2
Baniso -1Baniso -2Baniso -3
1--1.629 Å20.695 Å2-0.286 Å2
2--4.401 Å21.406 Å2
3----3.193 Å2
Refinement stepCycle: LAST / Resolution: 2.8→116.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21277 0 96 238 21611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01221966
X-RAY DIFFRACTIONr_bond_other_d0.0010.01620768
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.65429722
X-RAY DIFFRACTIONr_angle_other_deg0.41.57648047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45152674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.625596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.533103781
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.98210976
X-RAY DIFFRACTIONr_chiral_restr0.0570.23336
X-RAY DIFFRACTIONr_chiral_restr_other0.0040.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0224905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024743
X-RAY DIFFRACTIONr_nbd_refined0.210.25002
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.220847
X-RAY DIFFRACTIONr_nbtor_refined0.1810.210960
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.212102
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2645
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1560.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.213
X-RAY DIFFRACTIONr_nbd_other0.2590.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3310.22
X-RAY DIFFRACTIONr_mcbond_it3.9264.51610731
X-RAY DIFFRACTIONr_mcbond_other3.9264.51610728
X-RAY DIFFRACTIONr_mcangle_it6.088.10213354
X-RAY DIFFRACTIONr_mcangle_other6.088.10213355
X-RAY DIFFRACTIONr_scbond_it4.1734.79311235
X-RAY DIFFRACTIONr_scbond_other4.1734.79411236
X-RAY DIFFRACTIONr_scangle_it6.5828.67216360
X-RAY DIFFRACTIONr_scangle_other6.5818.67216361
X-RAY DIFFRACTIONr_lrange_it10.39454.4396552
X-RAY DIFFRACTIONr_lrange_other10.39554.43296544
X-RAY DIFFRACTIONr_ncsr_local_group_10.040.0511777
X-RAY DIFFRACTIONr_ncsr_local_group_20.0330.0512044
X-RAY DIFFRACTIONr_ncsr_local_group_30.0390.0511590
X-RAY DIFFRACTIONr_ncsr_local_group_40.0380.0512079
X-RAY DIFFRACTIONr_ncsr_local_group_50.0410.0511682
X-RAY DIFFRACTIONr_ncsr_local_group_60.0320.0512064
X-RAY DIFFRACTIONr_ncsr_local_group_70.0340.0511747
X-RAY DIFFRACTIONr_ncsr_local_group_80.0380.0511707
X-RAY DIFFRACTIONr_ncsr_local_group_90.040.0511596
X-RAY DIFFRACTIONr_ncsr_local_group_100.0440.0511749
X-RAY DIFFRACTIONr_ncsr_local_group_110.040.0511660
X-RAY DIFFRACTIONr_ncsr_local_group_120.0340.0511739
X-RAY DIFFRACTIONr_ncsr_local_group_130.0370.0511717
X-RAY DIFFRACTIONr_ncsr_local_group_140.0410.0511562
X-RAY DIFFRACTIONr_ncsr_local_group_150.040.0512028
X-RAY DIFFRACTIONr_ncsr_local_group_160.0370.0511692
X-RAY DIFFRACTIONr_ncsr_local_group_170.0260.0512038
X-RAY DIFFRACTIONr_ncsr_local_group_180.0320.0511710
X-RAY DIFFRACTIONr_ncsr_local_group_190.0430.0511572
X-RAY DIFFRACTIONr_ncsr_local_group_200.0390.0511631
X-RAY DIFFRACTIONr_ncsr_local_group_210.0370.0511606
X-RAY DIFFRACTIONr_ncsr_local_group_220.0370.0511631
X-RAY DIFFRACTIONr_ncsr_local_group_230.0370.0511706
X-RAY DIFFRACTIONr_ncsr_local_group_240.0360.0512032
X-RAY DIFFRACTIONr_ncsr_local_group_250.0350.0511734
X-RAY DIFFRACTIONr_ncsr_local_group_260.0330.0511732
X-RAY DIFFRACTIONr_ncsr_local_group_270.0340.0511793
X-RAY DIFFRACTIONr_ncsr_local_group_280.030.0511782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.040310.0501
12AX-RAY DIFFRACTIONLocal ncs0.040310.0501
23AX-RAY DIFFRACTIONLocal ncs0.033140.0501
24AX-RAY DIFFRACTIONLocal ncs0.033140.0501
35AX-RAY DIFFRACTIONLocal ncs0.039380.0501
36AX-RAY DIFFRACTIONLocal ncs0.039380.0501
47AX-RAY DIFFRACTIONLocal ncs0.037710.0501
48AX-RAY DIFFRACTIONLocal ncs0.037710.0501
59AX-RAY DIFFRACTIONLocal ncs0.040980.0501
510AX-RAY DIFFRACTIONLocal ncs0.040980.0501
611AX-RAY DIFFRACTIONLocal ncs0.031760.0501
612AX-RAY DIFFRACTIONLocal ncs0.031760.0501
713AX-RAY DIFFRACTIONLocal ncs0.033620.0501
714AX-RAY DIFFRACTIONLocal ncs0.033620.0501
815AX-RAY DIFFRACTIONLocal ncs0.03810.0501
816AX-RAY DIFFRACTIONLocal ncs0.03810.0501
917AX-RAY DIFFRACTIONLocal ncs0.040180.0501
918AX-RAY DIFFRACTIONLocal ncs0.040180.0501
1019AX-RAY DIFFRACTIONLocal ncs0.044240.0501
1020AX-RAY DIFFRACTIONLocal ncs0.044240.0501
1121AX-RAY DIFFRACTIONLocal ncs0.040340.0501
1122AX-RAY DIFFRACTIONLocal ncs0.040340.0501
1223AX-RAY DIFFRACTIONLocal ncs0.033820.0501
1224AX-RAY DIFFRACTIONLocal ncs0.033820.0501
1325AX-RAY DIFFRACTIONLocal ncs0.036740.0501
1326AX-RAY DIFFRACTIONLocal ncs0.036740.0501
1427AX-RAY DIFFRACTIONLocal ncs0.040530.0501
1428AX-RAY DIFFRACTIONLocal ncs0.040530.0501
1529AX-RAY DIFFRACTIONLocal ncs0.040410.0501
1530AX-RAY DIFFRACTIONLocal ncs0.040410.0501
1631AX-RAY DIFFRACTIONLocal ncs0.03720.0501
1632AX-RAY DIFFRACTIONLocal ncs0.03720.0501
1733AX-RAY DIFFRACTIONLocal ncs0.026330.05011
1734AX-RAY DIFFRACTIONLocal ncs0.026330.05011
1835AX-RAY DIFFRACTIONLocal ncs0.031690.0501
1836AX-RAY DIFFRACTIONLocal ncs0.031690.0501
1937AX-RAY DIFFRACTIONLocal ncs0.042660.0501
1938AX-RAY DIFFRACTIONLocal ncs0.042660.0501
2039AX-RAY DIFFRACTIONLocal ncs0.038640.05011
2040AX-RAY DIFFRACTIONLocal ncs0.038640.05011
2141AX-RAY DIFFRACTIONLocal ncs0.037350.0501
2142AX-RAY DIFFRACTIONLocal ncs0.037350.0501
2243AX-RAY DIFFRACTIONLocal ncs0.036740.0501
2244AX-RAY DIFFRACTIONLocal ncs0.036740.0501
2345AX-RAY DIFFRACTIONLocal ncs0.036640.0501
2346AX-RAY DIFFRACTIONLocal ncs0.036640.0501
2447AX-RAY DIFFRACTIONLocal ncs0.036280.0501
2448AX-RAY DIFFRACTIONLocal ncs0.036280.0501
2549AX-RAY DIFFRACTIONLocal ncs0.034580.0501
2550AX-RAY DIFFRACTIONLocal ncs0.034580.0501
2651AX-RAY DIFFRACTIONLocal ncs0.033120.0501
2652AX-RAY DIFFRACTIONLocal ncs0.033120.0501
2753AX-RAY DIFFRACTIONLocal ncs0.033720.0501
2754AX-RAY DIFFRACTIONLocal ncs0.033720.0501
2855AX-RAY DIFFRACTIONLocal ncs0.029960.0501
2856AX-RAY DIFFRACTIONLocal ncs0.029960.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.8-2.8730.3612680.32852910.3356560.9130.93498.2850.32
2.873-2.9510.3292900.29551050.29754810.9280.94798.43090.283
2.951-3.0370.3292710.26750160.2753730.9360.95598.39940.254
3.037-3.130.3312560.26948570.27251900.930.95398.51640.254
3.13-3.2330.3072570.25647490.25950860.9340.95998.42710.239
3.233-3.3460.2692400.22845860.2348950.9540.96898.59040.212
3.346-3.4720.2452590.21943740.22147160.960.9798.240.206
3.472-3.6140.2872460.22542370.22945520.9420.96998.48420.211
3.614-3.7750.2221820.20340910.20443400.9680.97598.45620.19
3.775-3.9590.2342310.18938840.19141590.9650.97898.94210.179
3.959-4.1720.2211920.18137400.18239670.9650.9899.11770.175
4.172-4.4250.2071960.16935360.17137620.9710.98299.20260.168
4.425-4.730.2011750.1633110.16235160.9740.98499.14680.16
4.73-5.1090.2131610.16730710.16932630.9680.98399.050.168
5.109-5.5950.2181680.17728360.17930370.9720.98298.91340.176
5.595-6.2540.2571310.17925240.18326940.960.98198.55230.179
6.254-7.2180.2331110.19222730.19424250.9710.97898.30930.195
7.218-8.8310.264930.20619090.20920310.9580.97498.57210.215
8.831-12.4540.208820.21314590.21315690.9750.97598.21540.231
12.454-116.4180.294440.2927900.2928730.9470.94795.53260.349
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)
10.47550.0678-0.12690.691-0.0310.2782-0.0108-0.05040.0112-0.1333-0.0057-0.08710.0698-0.02620.01650.26740.01970.0360.039-0.01950.234554.4081-58.080513.9088
20.24060.4039-0.23780.9294-0.26380.54770.10820.00790.0950.1231-0.0430.0634-0.0199-0.0166-0.06530.2473-0.02170.07020.0546-0.01050.258451.5088-17.278120.9812
30.848-0.2566-0.53550.40580.54661.0268-0.11170.179-0.0890.2353-0.17830.07460.2449-0.22990.290.238-0.17650.08180.1482-0.09090.242919.5839-65.533240.428
40.75410.3947-0.65710.4927-0.29180.97710.3886-0.04710.25670.1282-0.11140.1238-0.1662-0.0085-0.27720.3811-0.10110.21410.1241-0.12050.234920.9497-26.005653.9635
50.855-0.26010.35370.7427-0.14070.283-0.08010.05550.08420.16720.0115-0.1743-0.0192-0.06160.06870.2352-0.0169-0.07440.0562-0.01830.265317.6014-10.2719-7.4551
60.5817-0.08310.22780.566-0.13110.59130.14990.0219-0.1239-0.0769-0.0001-0.04710.06770.0096-0.14980.27330.0154-0.12830.0016-0.01760.278915.7624-51.0972-15.6146
70.66260.11790.26620.50990.07390.4954-0.0734-0.0280.0423-0.11210.01760.0913-0.139-0.01940.05580.21690.0496-0.04710.10880.00020.2244-17.1958-3.0751-33.83
80.3730.03570.29610.60130.09380.77490.12130.0369-0.10750.0310.02750.03430.1117-0.0158-0.14880.2393-0.0299-0.1210.0928-0.0490.2096-14.8804-42.2554-47.6948
Refinement TLS groupSelection: ALL

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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

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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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