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- PDB-5vjy: Crystal Structure of dUTP pyrophosphatase protein, from Naegleria... -

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Basic information

Entry
Database: PDB / ID: 5vjy
TitleCrystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri
ComponentsdUTP pyrophosphatase
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / dUTP pyrophosphatase
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri
Authors: Delker, S.L. / Abendroth, J. / Lorimer, D. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dUTP pyrophosphatase
B: dUTP pyrophosphatase
C: dUTP pyrophosphatase
D: dUTP pyrophosphatase
E: dUTP pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,32411
Polymers84,2165
Non-polymers1,1086
Water8,755486
1
A: dUTP pyrophosphatase
hetero molecules

A: dUTP pyrophosphatase
hetero molecules

A: dUTP pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3439
Polymers50,5293
Non-polymers8146
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10970 Å2
ΔGint-34 kcal/mol
Surface area15770 Å2
MethodPISA
2
B: dUTP pyrophosphatase
C: dUTP pyrophosphatase
D: dUTP pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1576
Polymers50,5293
Non-polymers6283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-37 kcal/mol
Surface area15190 Å2
MethodPISA
3
E: dUTP pyrophosphatase
hetero molecules

E: dUTP pyrophosphatase
hetero molecules

E: dUTP pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1576
Polymers50,5293
Non-polymers6283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-y-1,x-y+1,z1
crystal symmetry operation3_345-x+y-2,-x-1,z1
Buried area11100 Å2
ΔGint-40 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.640, 118.640, 98.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

21A-396-

HOH

31A-404-

HOH

41A-409-

HOH

51E-325-

HOH

61E-333-

HOH

71E-367-

HOH

81E-369-

HOH

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Components

#1: Protein
dUTP pyrophosphatase / NafoA.01242.a.B1


Mass: 16843.117 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Strain: ATCC 30863 / Plasmid: NafoA.01242.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1Z0YU86*PLUS
#2: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MCSG1 C12: 0.1 M Bis-Tris: HCl, pH 6.5 25 % (w/v) PEG 3350 cryo:15% Ethylene Glycol. PW37974 22.5mg/mL, 0.4+0.4 puck xbp1-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→34.248 Å / Num. obs: 53461 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.912 % / Biso Wilson estimate: 30.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.058 / Χ2: 1.027 / Net I/σ(I): 26.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.058.9190.5334.1239600.9160.565100
2.05-2.118.9350.4295.1538330.9470.455100
2.11-2.178.9340.3446.4837200.9640.365100
2.17-2.248.9440.2758.0436600.9770.292100
2.24-2.318.9470.2349.5535090.9810.248100
2.31-2.398.9520.18811.833660.9880.199100
2.39-2.488.960.15514.0833180.9910.165100
2.48-2.588.9650.12916.6931540.9940.137100
2.58-2.78.9690.11219.130350.9960.118100
2.7-2.838.9540.08424.6729090.9970.09100
2.83-2.988.9630.06431.0827360.9980.068100
2.98-3.168.930.05337.1126280.9990.056100
3.16-3.388.920.04147.0124560.9990.044100
3.38-3.658.9250.03454.4622910.9990.036100
3.65-48.950.02863.12210910.03100
4-4.478.8910.02469.22191010.026100
4.47-5.168.8690.02372.35170810.025100
5.16-6.328.7860.02570.79141410.026100
6.32-8.948.5890.02372.14112410.025100
8.94-34.2487.5280.02174.9762110.02398.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2733refinement
PDB_EXTRACT3.22data extraction
MoRDaphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4oop
Resolution: 2→34.248 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.62
RfactorNum. reflection% reflection
Rfree0.1765 2050 3.84 %
Rwork0.1423 --
obs0.1436 53440 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.31 Å2 / Biso mean: 39.7166 Å2 / Biso min: 13.84 Å2
Refinement stepCycle: final / Resolution: 2→34.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 74 498 5568
Biso mean--47.79 42.35 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065310
X-RAY DIFFRACTIONf_angle_d0.8797231
X-RAY DIFFRACTIONf_chiral_restr0.064817
X-RAY DIFFRACTIONf_plane_restr0.005947
X-RAY DIFFRACTIONf_dihedral_angle_d10.9693218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.04650.21951390.182133983537
2.0465-2.09770.20051290.171634453574
2.0977-2.15440.22491290.168334063535
2.1544-2.21780.22531390.155633963535
2.2178-2.28930.1931400.15934083548
2.2893-2.37110.19431390.150334383577
2.3711-2.4660.19191250.146434153540
2.466-2.57820.18571540.148134113565
2.5782-2.71410.21411270.161234383565
2.7141-2.88410.19231260.150634273553
2.8841-3.10660.1941470.159234063553
3.1066-3.4190.14971600.143834013561
3.419-3.91310.17231420.134334403582
3.9131-4.92780.14651320.111234573589
4.9278-34.25340.1591220.13835043626
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)
11.85631.1252-2.09171.66850.71098.03540.1058-0.7295-0.37750.6430.02620.0640.0889-0.4439-0.12420.58740.0326-0.02440.42630.15110.2678-58.249818.283920.2404
22.49060.29850.74673.04392.82316.34060.0332-0.0859-0.43940.4323-0.00710.23261.20330.0346-0.0170.50630.0093-0.01850.18160.08730.2872-55.67558.7136.4097
35.68222.45090.57367.17742.71875.593-0.052-0.39250.20431.08020.0885-1.64140.23110.3667-0.06720.36270.0913-0.16270.33090.07120.4383-46.390122.224410.7769
41.7979-0.34210.67812.36230.37383.28320.01970.0902-0.17740.02370.0165-0.01620.26350.0616-0.01250.1535-0.00240.00980.13610.00160.1201-56.41619.3606-2.0641
52.92680.5422-1.58192.0577-0.95634.7029-0.0901-0.0608-0.08390.04940.0362-0.19230.02250.13520.02950.13680.0016-0.00150.1117-0.00740.1004-52.662829.0826-1.7673
61.5222-0.29720.01133.5833-1.26516.23570.0509-0.076-0.1337-0.1024-0.03290.07860.07060.119-0.0230.1127-0.0114-0.01220.1275-0.0150.1196-59.758423.3426-2.9864
78.5244-3.94020.54437.52750.89444.5876-0.1780.1323-0.6199-0.45350.1089-0.40820.3680.02480.12160.20090.02150.03720.1604-0.04540.1994-48.723216.641-8.539
84.7583-1.909-4.55666.04975.53428.90960.0008-0.2866-0.25890.13350.0231-0.2058-0.28980.3194-0.10770.20790.0261-0.02870.21260.02190.0664-54.288426.09876.7497
92.71510.05130.92741.2199-1.35265.0245-0.2219-0.90210.72050.43570.39550.3631-0.6502-0.8276-0.16710.38260.04680.10130.4609-0.04430.3194-77.450540.715215.1548
109.66444.2053-0.75342.934-3.54159.44670.1768-0.4427-0.78270.2826-0.5087-0.29680.70340.37280.24860.34220.0185-0.02980.2357-0.01030.3111-58.04260.4843-10.0004
111.85781.4556-1.39546.0651-5.81685.5914-0.11470.0979-0.22250.1857-0.2261-0.8626-0.21430.99760.44960.265-0.03070.06760.3903-0.08430.4346-49.35259.3995-21.4608
123.25730.3591-1.37392.8176-1.30015.24550.02360.14240.3183-0.120.0648-0.1239-0.06190.0918-0.08610.2077-0.0380.02450.2367-0.06350.2862-61.78815.9176-22.8928
133.61080.5409-1.08912.2609-1.50383.9237-0.14810.2579-0.0613-0.59640.0342-0.46250.42310.21870.14440.29080.01250.06650.2258-0.11040.23-59.14876.6329-25.9475
142.78920.50490.37452.7877-0.82382.3176-0.00490.2640.0356-0.08290.07710.02530.21110.0249-0.07150.2348-0.02320.02350.2053-0.08810.2141-66.50549.189-25.2126
153.0180.8844-0.08343.2647-0.99943.6943-0.01920.34370.3935-0.29960.0609-0.0788-0.1490.2641-0.02890.2539-0.01470.04460.2293-0.03640.2722-65.372715.5628-28.4761
164.93941.82592.19796.71243.89955.68330.08260.0531-0.92270.5126-0.12750.50621.0212-0.6411-0.08110.6675-0.1470.10380.33-0.07190.5712-80.3459-16.066-21.4437
174.1288-3.26712.95779.2721-4.92018.6622-0.2896-0.60710.49910.82170.08470.6356-0.098-0.30.18190.3315-0.06010.15610.351-0.16560.5168-86.945615.7342-6.846
180.0871-0.574-0.45887.70073.67652.6297-0.4806-0.0152-0.92440.856-0.16911.04551.0834-0.53380.49760.5141-0.12340.25010.3766-0.16890.9042-91.2134.7176-13.9075
193.3313-0.73130.66692.4485-0.69951.7090.04620.2540.2258-0.1625-0.09320.53770.0627-0.09670.04190.2408-0.0286-0.02970.2565-0.08070.3952-84.293714.5361-23.2633
206.80563.48061.30116.0907-0.70842.997-0.1877-0.6035-0.44930.06180.0969-0.89960.35150.57070.08370.30080.04-0.02870.2506-0.04420.2899-54.67464.1682-13.6018
215.6636-1.30761.23682.0828-1.91782.0392-0.2209-0.2098-0.94820.57290.05660.49320.8908-0.740.12880.6241-0.13360.09820.3593-0.03210.561-79.4455-14.5642-15.5338
224.1737-0.44640.74294.4346-1.60597.408-0.02780.6716-1.0047-0.4619-0.52550.48251.2426-0.81450.28390.5056-0.12570.00010.4928-0.24140.5871-83.4277-16.9345-31.694
234.26164.9935.75766.51436.32948.43090.36210.3175-1.27250.41830.3704-0.45080.50830.1299-0.76330.39390.0289-0.02220.3325-0.12720.428-68.6669-12.1645-25.5602
241.0869-0.26240.5093.2145-0.32052.6301-0.1250.5676-0.3595-0.46250.07880.52440.4172-0.32730.07150.4398-0.136-0.03170.4939-0.19340.4517-80.238-5.4744-34.3538
253.03781.5573-1.7053.8654-2.44813.6093-0.13140.5213-0.1629-0.38880.20480.04250.2486-0.05340.00040.3699-0.0652-0.01220.3189-0.13140.2641-72.37121.4366-31.9109
263.73392.65442.83647.95211.97682.1587-0.07680.1235-0.27530.0841-0.20510.92130.3215-0.61060.24610.2799-0.08630.02510.3603-0.15330.5867-86.2204-4.8563-25.0484
277.33112.36161.94297.6881-1.18244.6177-0.54341.34750.3661-1.19020.0650.1730.0324-0.04750.48750.5438-0.0194-0.06550.5447-0.06230.3224-76.62525.5031-41.456
281.3165-0.32890.25081.58-0.3851.0744-0.43930.6029-0.4851-0.6009-0.12720.11730.178-0.26840.26270.583-0.15520.04130.4198-0.20680.3823-74.5597-5.1604-33.6238
295.1553-1.9695-1.17231.51181.99234.4547-0.2545-0.81630.6360.97450.22770.7976-0.1247-0.25950.08220.5138-0.04720.18180.4354-0.13530.5761-85.910912.6064-5.592
309.37893.01170.23911.9732-0.11942.0308-0.24560.87190.8857-1.6789-0.4564-0.7135-0.54580.21050.73170.7633-0.075-0.00490.45570.14230.5838-111.379213.7125-38.2368
315.5453-1.29522.65229.40083.7323.7139-0.61320.19271.1615-0.64930.5227-0.1836-1.01260.56030.08470.3302-0.07450.0360.30320.07390.7373-105.870622.4069-24.9564
322.96692.2377-1.06164.3898-1.82596.1358-0.0621-0.14560.26740.1463-0.0488-0.3534-0.32950.33260.10550.21510.0153-0.04650.2383-0.01110.5065-108.065211.0106-19.5896
333.9353-1.0073.26544.2256-3.70987.4344-0.0439-0.26280.02950.22710.029-0.2653-0.0697-0.28580.08290.1961-0.0215-0.02280.2344-0.00110.4005-111.15562.5217-17.3809
346.10942.5456-0.50485.1281-2.77958.4733-0.01450.31821.2381-0.21360.09821.0679-0.4531-0.5106-0.10050.23850.0509-0.00440.27380.03210.6444-118.230415.3292-24.8345
357.05174.4092-3.77356.0791-0.63482.95790.6627-1.04940.08980.9252-0.6197-0.3161-0.45520.5876-0.04310.3645-0.0975-0.10.4046-0.00410.397-107.49048.5313-8.6543
369.28782.21756.55055.81642.40064.8466-0.26990.58090.17040.07030.2062-0.4329-0.22040.85450.07130.2312-0.0512-0.00950.29510.02950.3402-110.99185.8394-25.3029
378.03980.1983-1.44924.371.66635.47860.31790.75570.0233-0.2004-0.27431.11220.2929-0.905-0.05560.4065-0.0103-0.20650.46750.00670.5965-138.06250.2639-33.7562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 7 )A0 - 7
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 16 )A8 - 16
3X-RAY DIFFRACTION3chain 'A' and (resid 17 through 26 )A17 - 26
4X-RAY DIFFRACTION4chain 'A' and (resid 27 through 58 )A27 - 58
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 78 )A59 - 78
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 101 )A79 - 101
7X-RAY DIFFRACTION7chain 'A' and (resid 102 through 108 )A102 - 108
8X-RAY DIFFRACTION8chain 'A' and (resid 109 through 117 )A109 - 117
9X-RAY DIFFRACTION9chain 'A' and (resid 118 through 130 )A118 - 130
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 7 )B0 - 7
11X-RAY DIFFRACTION11chain 'B' and (resid 8 through 16 )B8 - 16
12X-RAY DIFFRACTION12chain 'B' and (resid 17 through 42 )B17 - 42
13X-RAY DIFFRACTION13chain 'B' and (resid 43 through 58 )B43 - 58
14X-RAY DIFFRACTION14chain 'B' and (resid 59 through 90 )B59 - 90
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 117 )B91 - 117
16X-RAY DIFFRACTION16chain 'B' and (resid 118 through 131 )B118 - 131
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 16 )C0 - 16
18X-RAY DIFFRACTION18chain 'C' and (resid 17 through 26 )C17 - 26
19X-RAY DIFFRACTION19chain 'C' and (resid 27 through 117 )C27 - 117
20X-RAY DIFFRACTION20chain 'C' and (resid 118 through 131 )C118 - 131
21X-RAY DIFFRACTION21chain 'D' and (resid 0 through 7 )D0 - 7
22X-RAY DIFFRACTION22chain 'D' and (resid 8 through 16 )D8 - 16
23X-RAY DIFFRACTION23chain 'D' and (resid 17 through 26 )D17 - 26
24X-RAY DIFFRACTION24chain 'D' and (resid 27 through 58 )D27 - 58
25X-RAY DIFFRACTION25chain 'D' and (resid 59 through 78 )D59 - 78
26X-RAY DIFFRACTION26chain 'D' and (resid 79 through 90 )D79 - 90
27X-RAY DIFFRACTION27chain 'D' and (resid 91 through 101 )D91 - 101
28X-RAY DIFFRACTION28chain 'D' and (resid 102 through 117 )D102 - 117
29X-RAY DIFFRACTION29chain 'D' and (resid 118 through 130 )D118 - 130
30X-RAY DIFFRACTION30chain 'E' and (resid 0 through 7 )E0 - 7
31X-RAY DIFFRACTION31chain 'E' and (resid 8 through 16 )E8 - 16
32X-RAY DIFFRACTION32chain 'E' and (resid 17 through 58 )E17 - 58
33X-RAY DIFFRACTION33chain 'E' and (resid 59 through 78 )E59 - 78
34X-RAY DIFFRACTION34chain 'E' and (resid 79 through 90 )E79 - 90
35X-RAY DIFFRACTION35chain 'E' and (resid 91 through 108 )E91 - 108
36X-RAY DIFFRACTION36chain 'E' and (resid 109 through 117 )E109 - 117
37X-RAY DIFFRACTION37chain 'E' and (resid 118 through 131 )E118 - 131

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