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- PDB-3dh9: Crystal Structure of Drosophila Thioredoxin Reductase, wild-type -

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Basic information

Entry
Database: PDB / ID: 3dh9
TitleCrystal Structure of Drosophila Thioredoxin Reductase, wild-type
ComponentsThioredoxin reductase 1
KeywordsOXIDOREDUCTASE / rossmann / flavoprotein / Alternative initiation / FAD / Mitochondrion / NADP / Redox-active center / Transit peptide
Function / homology
Function and homology information


: / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / antioxidant activity / cell redox homeostasis / determination of adult lifespan / flavin adenine dinucleotide binding ...: / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / antioxidant activity / cell redox homeostasis / determination of adult lifespan / flavin adenine dinucleotide binding / protein homodimerization activity / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain ...Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase 1, mitochondrial
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsEckenroth, B.E. / Hondal, R.J. / Everse, S.J.
CitationJournal: To be Published
Title: Crystal Structure of Drosophila Thioredoxin Reductase, wild-type
Authors: Eckenroth, B.E. / Hondal, R.J. / Everse, S.J.
History
DepositionJun 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase 1
B: Thioredoxin reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4424
Polymers104,8712
Non-polymers1,5712
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-68 kcal/mol
Surface area37390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.971, 150.971, 267.706
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A500
2114B500
1214A5 - 163
2214B5 - 163
1314A291 - 363
2314B291 - 363
1124A164 - 290
2124B164 - 290
1134A364 - 486
2134B364 - 486

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Thioredoxin reductase 1 / / TrxR-1


Mass: 52435.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Trxr-1, GR, CG2151 / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: P91938, thioredoxin-disulfide reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES, 20% PEG 4000, pH 5.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 10, 2008 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→32 Å / Num. obs: 55708 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.089 / Χ2: 0.961 / Net I/σ(I): 8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 5.38 / Num. unique all: 5517 / Χ2: 1.194 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Translation2.26 Å31.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
Custom pXSCAN motion control software coupled with the Mar345 data collection softwaredata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→31.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.811 / SU B: 11.708 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 5611 10.1 %RANDOM
Rwork0.177 ---
obs0.184 55705 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 433.43 Å2 / Biso mean: 14.901 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.25→31.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 0 106 512 8002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0227652
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.98810414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9615962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56324.167312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.558151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.261542
X-RAY DIFFRACTIONr_chiral_restr0.1650.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025720
X-RAY DIFFRACTIONr_nbd_refined0.2320.23714
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2559
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.213
X-RAY DIFFRACTIONr_mcbond_it0.9531.54940
X-RAY DIFFRACTIONr_mcangle_it1.49227676
X-RAY DIFFRACTIONr_scbond_it2.60133239
X-RAY DIFFRACTIONr_scangle_it3.9084.52738
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11807MEDIUM POSITIONAL0.440.5
11807MEDIUM THERMAL1.082
2979MEDIUM POSITIONAL0.190.5
2979MEDIUM THERMAL0.882
3959MEDIUM POSITIONAL0.150.5
3959MEDIUM THERMAL1.012
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 394 -
Rwork0.185 3708 -
all-4102 -
obs--100 %
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)
11.52750.68211.3235.14211.51513.04810.34210.1912-0.1469-0.3724-0.16440.2180.135-0.283-0.1778-0.0282-0.0572-0.0510.0761-0.0301-0.086478.62166.70638.692
24.69072.0044.32051.47943.21146.9712-0.02540.0097-0.02130.1712-0.0314-0.083-0.2825-0.31050.05690.0362-0.04170.067-0.00420.0047-0.063888.143174.3855.467
31.15140.07791.58953.140.45742.2334-0.1591-0.0678-0.0672-0.04190.10330.0413-0.6381-0.18910.05570.0948-0.120.0612-0.0257-0.0181-0.0763102.486178.16170.057
416.0061-0.31546.62230.3748-0.78038.7444-0.4759-0.68051.04430.5235-0.2202-0.3069-1.4607-0.4530.69610.267-0.1069-0.0606-0.1547-0.02050.053598.78187.62561.685
52.69553.77863.93857.83159.95213.50060.1380.3001-0.16680.02020.027-0.1246-0.23360.2777-0.165-0.0481-0.09880.03740.03210.0075-0.07592.332173.24542.809
65.2751-0.18451.22062.4877-0.83061.16560.30260.264-0.0082-0.42670.06230.05350.22390.2155-0.3648-0.0223-0.0579-0.07550.127-0.0634-0.11578.182165.69532.709
714.512312.4053-1.861816.3175-1.304810.15120.15980.70080.4156-0.50450.47530.61440.05760.4571-0.6351-0.0752-0.0682-0.07560.11720.0628-0.089270.674171.04629.155
81.201-0.30790.79230.5519-0.87881.48810.0950.1984-0.0794-0.2617-0.03030.48940.0565-0.4381-0.0647-0.0949-0.032-0.04470.20490.0362-0.015569.673172.5642.116
92.51770.3661-1.26730.14250.2622.86810.22770.1990.13460.0352-0.181-0.0739-0.7432-0.1335-0.04680.06860.05660.0751-0.03790.0517-0.035878.418186.7552.404
102.71480.442-0.79991.0833-0.58281.5434-0.04810.01570.26690.04620.15940.1115-0.2992-0.1245-0.11120.08370.04040.0812-0.0547-0.0275-0.048281.995184.31263.271
111.52391.2144-0.18163.7743-1.25181.2102-0.0768-0.2002-0.08670.2750.18230.1375-0.2643-0.2469-0.1056-0.02180.04740.09750.0237-0.0257-0.076477.625175.7573.06
124.76643.3765-3.88787.3921-4.60868.1426-0.1476-0.08070.78510.4550.1690.1459-0.6425-0.4185-0.02130.13060.28820.0968-0.12620.03530.122171.945194.75462.899
130.50950.22940.32111.0337-0.67122.48960.00130.15620.30220.25210.20810.4711-0.5402-0.6798-0.20940.02090.14920.14520.03750.03060.092870.029186.01561.127
143.8107-0.31812.78212.46390.40232.26520.2831-0.5284-0.5231-0.03640.20540.62080.4668-0.5819-0.4885-0.0969-0.224-0.04380.19450.11260.102165.636162.39746.869
151.16670.76372.86194.46323.59037.8610.3188-0.0825-0.23260.07490.12740.31070.7287-0.6285-0.4461-0.0039-0.1845-0.07390.02040.04380.01778.643156.84153.418
163.89471.1255-0.97431.1946-0.63910.89950.0235-0.0813-0.22370.09090.14560.10820.0163-0.3787-0.169-0.0811-0.03920.07890.01530.0377-0.023776.682159.52577.212
173.6152.47750.98083.5621-0.18881.4797-0.2157-0.1151-0.02540.00720.23580.1197-0.0989-0.2748-0.02-0.0515-0.00720.1045-0.07030.0155-0.105785.667162.62579.277
181.24930.8043-0.54591.1253-0.89710.7286-0.01910.12930.04980.11270.09250.1834-0.0549-0.2065-0.0735-0.0157-0.05790.0813-0.03-0.025-0.003485.009158.99569.609
196.07973.01840.6182.54820.44560.95240.0103-0.2734-0.24030.03440.06160.08380.1155-0.0989-0.07180.0257-0.04650.0564-0.08720.0297-0.033189.656152.47275.465
206.3801-0.5533-5.4985.9346-0.28368.32040.1263-1.179-0.18160.27030.0942-0.2099-0.13090.5358-0.2206-0.0229-0.07610.10850.05960.0401-0.101282.388159.31687.321
213.2203-0.39772.2492.21371.4662.97540.2754-0.2269-0.1949-0.0332-0.12030.167-0.235-0.6208-0.155-0.0399-0.09860.01890.11280.0232-0.038178.026170.01348.905
222.81050.307-2.40310.8397-0.07953.9390.1104-0.1430.04250.0166-0.10290.0940.18240.0973-0.00760.1003-0.01610.0496-0.1442-0.0016-0.085299.958147.20198.241
234.22611.2331-1.12511.1535-0.36811.4742-0.0742-0.3241-0.01850.14310.0512-0.10620.21080.29940.0230.02090.03190.0349-0.0659-0.0361-0.1058111.062155.52893.655
240.0727-0.38330.13133.179-1.78821.2746-0.10.0017-0.0423-0.26540.17710.17780.13680.0366-0.0770.038-0.03670.0449-0.0146-0.0463-0.0354107.765164.70376.451
252.5581-0.20681.88231.5922-3.19057.2445-0.13220.26530.0060.0417-0.0281-0.15660.09210.44250.16030.1365-0.10050.0425-0.0687-0.0388-0.0737103.778178.20762.389
262.2264-1.39994.338310.6049-7.251710.6744-0.09720.5390.4708-0.047-0.2666-0.2791-0.38811.37450.3638-0.0235-0.14170.02250.01150.02190.0282114.073177.71573.971
273.67713.9618-7.53525.2385-7.611415.7063-0.0452-0.05340.05850.31330.0871-0.0421-0.32820.2198-0.0420.07670.02920.0199-0.0881-0.0373-0.0496104.449165.98992.137
282.641-0.54560.96753.20390.08281.54760.0762-0.388-0.12180.33520.09590.15340.12620.1235-0.17210.10960.05070.0421-0.12290.0154-0.1566106.199148.632102.259
293.5996-0.0627-2.23950.8562-0.84074.1826-0.0416-0.2269-0.05050.21230.1594-0.24220.11250.3728-0.11770.01250.087-0.0115-0.1486-0.0512-0.0633115.814148.07895.65
303.00590.6896-0.65513.33020.11780.968-0.1681-0.24930.2749-0.0560.098-0.239-0.05350.34270.0702-0.07570.00530.0410.0372-0.0612-0.017123.592161.17281.955
311.39220.3298-0.28122.3064-0.48161.45340.034-0.05980.001-0.0674-0.0951-0.15630.05440.3360.061-0.0357-0.00440.11080.0378-0.0397-0.0452118.667159.16169.581
323.48294.20930.91235.09380.97362.7434-0.03990.3534-0.2344-0.11540.1964-0.1601-0.00930.3657-0.15660.01050.01610.134-0.0172-0.0551-0.0558113.001156.42759.373
330.2538-0.5738-0.22631.34710.14062.9690.0168-0.0070.0008-0.23340.0378-0.45730.07860.4965-0.0545-0.15340.04080.15680.0865-0.05850.0877129.968155.47871.044
343.46790.7845-0.19333.44031.10462.52670.08790.0118-0.44580.15470.0377-0.23970.44370.2704-0.12550.10450.07220.0018-0.2452-0.0193-0.0188109.611136.29591.028
354.8234-2.55531.17366.3551-2.00163.5411-0.08840.2841-0.2244-0.20360.01390.01890.36040.04190.07440.0360.00210.0401-0.1544-0.0595-0.0657104.644145.15581.651
362.71731.2477-2.1712.3616-5.85814.9455-0.08430.0998-0.1636-0.21560.26860.17031.0156-0.4009-0.18420.1041-0.0630.024-0.20720.0117-0.038493.828141.20786.706
371.10461.1592-0.61451.4567-0.67362.2895-0.11160.054-0.3224-0.2321-0.0588-0.20070.52320.11160.17050.12840.02210.1255-0.1056-0.07840.0371101.801146.11560.76
380.9812-0.68920.3357.6833-1.64773.2791-0.11920.33150.003-0.1227-0.0822-0.01280.10490.07510.2014-0.0256-0.09830.0618-0.013-0.0584-0.096102.1165.48754.068
396.55610.44130.17177.25223.30331.5047-0.68850.5286-0.8757-0.87880.45750.07230.5673-0.27750.23110.3438-0.20290.089-0.0387-0.0905-0.003292.747140.73356.439
400.6062-0.2437-0.3471.358-0.44271.7032-0.08690.1087-0.1632-0.2440.07140.05680.2886-0.05490.01550.053-0.09240.0514-0.079-0.0569-0.023391.656152.89261.861
416.35331.9654-3.90132.2052.447510.7581-0.14970.63480.1531-0.4988-0.17680.4649-0.1963-0.28310.32650.2479-0.1277-0.0268-0.023-0.0992-0.113897.209150.11447.158
423.35291.05290.9552.63580.94950.45510.0837-0.1127-0.163-0.14520.18910.07090.48530.0496-0.27270.05990.01380.0448-0.069-0.0354-0.0293109.253152.33885.587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 581 - 54
2X-RAY DIFFRACTION2AA59 - 6955 - 65
3X-RAY DIFFRACTION3AA70 - 8766 - 83
4X-RAY DIFFRACTION4AA88 - 9984 - 95
5X-RAY DIFFRACTION5AA100 - 11896 - 114
6X-RAY DIFFRACTION6AA119 - 134115 - 130
7X-RAY DIFFRACTION7AA135 - 146131 - 142
8X-RAY DIFFRACTION8AA147 - 168143 - 164
9X-RAY DIFFRACTION9AA169 - 183165 - 179
10X-RAY DIFFRACTION10AA184 - 218180 - 214
11X-RAY DIFFRACTION11AA219 - 245215 - 241
12X-RAY DIFFRACTION12AA246 - 265242 - 261
13X-RAY DIFFRACTION13AA266 - 293262 - 289
14X-RAY DIFFRACTION14AA294 - 335290 - 331
15X-RAY DIFFRACTION15AA336 - 371332 - 367
16X-RAY DIFFRACTION16AA372 - 401368 - 397
17X-RAY DIFFRACTION17AA402 - 426398 - 422
18X-RAY DIFFRACTION18AA427 - 448423 - 444
19X-RAY DIFFRACTION19AA449 - 472445 - 468
20X-RAY DIFFRACTION20AA473 - 486469 - 482
21X-RAY DIFFRACTION21AC5001
22X-RAY DIFFRACTION22BB5 - 301 - 26
23X-RAY DIFFRACTION23BB31 - 5927 - 55
24X-RAY DIFFRACTION24BB60 - 7256 - 68
25X-RAY DIFFRACTION25BB73 - 8769 - 83
26X-RAY DIFFRACTION26BB88 - 10284 - 98
27X-RAY DIFFRACTION27BB103 - 11799 - 113
28X-RAY DIFFRACTION28BB118 - 139114 - 135
29X-RAY DIFFRACTION29BB140 - 168136 - 164
30X-RAY DIFFRACTION30BB169 - 184165 - 180
31X-RAY DIFFRACTION31BB185 - 225181 - 221
32X-RAY DIFFRACTION32BB226 - 243222 - 239
33X-RAY DIFFRACTION33BB244 - 291240 - 287
34X-RAY DIFFRACTION34BB292 - 324288 - 320
35X-RAY DIFFRACTION35BB325 - 340321 - 336
36X-RAY DIFFRACTION36BB341 - 361337 - 357
37X-RAY DIFFRACTION37BB362 - 397358 - 393
38X-RAY DIFFRACTION38BB398 - 414394 - 410
39X-RAY DIFFRACTION39BB415 - 426411 - 422
40X-RAY DIFFRACTION40BB427 - 472423 - 468
41X-RAY DIFFRACTION41BB473 - 486469 - 482
42X-RAY DIFFRACTION42BD5001

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