[English] 日本語
Yorodumi
- PDB-4qc9: Crystal structure of Vaccinia virus uracil-DNA glycosylase mutant 3GD4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qc9
TitleCrystal structure of Vaccinia virus uracil-DNA glycosylase mutant 3GD4
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / DNA repair enzyme / component of processivity factor / A20 / DNA / Poxvirus
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / DNA repair / DNA binding
Similarity search - Function
Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.259 Å
AuthorsSartmatova, D. / Nash, T. / Schormann, N. / Nuth, M. / Ricciardi, R. / Banerjee, S. / Chattopadhyay, D.
Citation
Journal: To be Published
Title: Crystal structure of Vaccinia virus uracil-DNA glycosylase mutant 3GD4
Authors: Sartmatova, D. / Nash, T. / Schormann, N. / Nuth, M. / Ricciardi, R. / Banerjee, S. / Chattopadhyay, D.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization and preliminary X-ray diffraction analysis of three recombinant mutants of Vaccinia virus uracil DNA glycosylase.
Authors: Sartmatova, D. / Nash, T. / Schormann, N. / Nuth, M. / Ricciardi, R. / Banerjee, S. / Chattopadhyay, D.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Source and taxonomy
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uracil-DNA glycosylase
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,86417
Polymers100,8884
Non-polymers97713
Water4,252236
1
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,10411
Polymers50,4442
Non-polymers6619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-52 kcal/mol
Surface area19870 Å2
MethodPISA
2
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7606
Polymers50,4442
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-38 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.378, 93.378, 285.182
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Uracil-DNA glycosylase / UDG


Mass: 25221.875 Da / Num. of mol.: 4 / Mutation: D17N, E171G, S172G, P173G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Western Reserve, D4R, VACWR109 / Gene: ACAM3000_MVA_101, D4, MVA101R, UNG / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: Q91UM2, UniProt: P04303*PLUS, uracil-DNA glycosylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2 M lithium sulfate, 50 mM MES, 5 mM magnesium chloride, 5% ethylene glycol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2012 / Details: Mirrors
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.259→47.53 Å / Num. all: 68116 / Num. obs: 68116 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 20.2
Reflection shellResolution: 2.259→2.38 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.2 / Num. unique all: 9832 / Rsym value: 0.508 / % possible all: 99.7

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
RAPDdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DOF, CHAIN A

4dof


Resolution: 2.259→46.61 Å / SU ML: 0.34 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 25.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 3452 5.07 %RANDOM
Rwork0.1847 ---
all0.1869 68031 --
obs0.1869 68031 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.76 Å2 / Biso mean: 68.3688 Å2 / Biso min: 40.54 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.259→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6983 0 57 236 7276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_refined_d0.003
X-RAY DIFFRACTIONf_angle_refined_deg0.791
X-RAY DIFFRACTIONf_chiral_restr0.031
X-RAY DIFFRACTIONf_gen_planes_refined0.003
X-RAY DIFFRACTIONf_dihedral_angle_1_deg11.311
LS refinement shellResolution: 2.259→2.29 Å
RfactorNum. reflection% reflection
Rfree0.377 127 -
Rwork0.3294 --
obs-2643 99 %
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)
14.3287-4.099-4.58379.58485.00284.6633-0.2325-0.90820.1613-0.4281-0.0526-1.3584-0.29282.05010.46650.62640.0117-0.07340.87710.18720.761358.1135-15.631227.8577
25.12370.2932-4.82242.1769-0.57464.018-0.2751-0.31010.0667-0.0337-0.0543-0.04040.21731.11610.37510.5369-0.0186-0.03170.94420.09250.619454.0406-15.836127.6621
39.25011.2232-6.36429.19941.98125.25070.1180.37360.6492-0.07470.2592-0.5828-0.71220.6196-0.4150.657-0.1844-0.10020.80860.04690.616753.9615-7.31423.8523
44.51955.6007-5.11088.8226-5.91796.07421.1495-0.81350.64481.0544-0.62790.2855-1.61570.9233-0.510.8116-0.2244-0.03370.9154-0.0820.618146.5686-7.579735.075
59.7145-5.7712-5.42924.66224.1684.5594-0.0275-0.2126-0.18030.476-0.11950.07810.180.4050.1360.6493-0.1075-0.10040.75810.07320.501441.9545-19.65236.2046
66.23441.5746-1.56872.1094-0.29591.9081-0.0358-0.4619-0.6150.1364-0.64660.14350.8921.10170.54930.5135-0.0341-0.05880.72340.08470.447450.1539-19.43621.4055
73.527-2.67010.77645.66751.31053.23680.28190.18940.3196-0.0659-0.1715-0.3867-0.59030.456-0.04730.4414-0.105-0.03470.62840.01820.458241.0709-18.854516.9955
80.87370.43430.13496.24294.41427.10910.0847-0.345-0.23570.6992-0.18320.09910.1586-0.14620.08960.4916-0.0528-0.00310.6180.04380.445234.6138-29.631721.1339
98.95184.77042.8717.12870.96974.51470.0046-0.5143-0.3120.4482-0.19520.21770.109-0.03240.27760.45740.05070.05480.712-0.08430.5534.6574-35.66910.2719
100.47991.5281-0.17353.19372.0921.61040.0935-0.1897-0.0415-0.07710.2002-0.2336-0.28650.5147-0.2040.5217-0.0164-0.02880.76360.04020.501241.0632-19.800920.5484
114.85344.3018-6.77244.1101-6.04648.99310.3019-0.43330.80580.302-0.23070.7469-0.66860.09190.02210.5934-0.0857-0.02990.632-0.01490.567237.0124-11.227830.3013
125.7084.43531.83254.68221.60076.3353-0.0877-0.32320.2226-0.2684-0.2966-0.0393-0.04110.41360.40380.3304-0.0565-0.03750.65010.05320.472143.7474-11.254413.3739
132.4592.4089-4.19017.4806-1.47678.88620.011-0.41360.2843-0.0166-0.03390.7338-0.7847-0.38280.02560.5566-0.00980.05150.8773-0.05720.617229.5418-11.338617.2308
145.1244-4.35614.58214.1701-4.01184.5579-0.55020.1715-0.16261.7431-0.7728-1.334-1.00470.17781.11810.6804-0.0385-0.08550.77330.09330.62438.8388-5.37726.943
155.12814.8917-1.60525.4222-3.15447.83820.82860.09510.18220.5828-0.67540.6106-0.05940.3097-0.14190.48130.0616-0.02840.7064-0.07990.608228.6354-17.617313.7811
160.7432-0.7259-1.35670.78181.4152.529-0.63290.4171.78910.76041.18090.7870.9462-0.5297-0.82720.6475-0.0793-0.14190.92770.12471.396420.0924-23.113114.7482
175.2619-3.78873.47313.2062-1.654610.01410.2803-0.4129-0.25750.33750.59481.02310.1491-1.8335-0.46920.5429-0.1843-0.04780.87610.02080.745825.3672-24.57087.8967
187.51262.2773-5.13038.6639-5.6745.73720.5695-1.12290.2414-0.2-0.25580.41040.7481.0122-0.21910.52390.0191-0.1260.6448-0.0460.393734.8661-20.28173.0792
192.4989-2.39452.17982.3186-1.99292.30121.17050.1892-0.3136-1.2164-0.5331-1.79751.05711.1113-0.60390.6864-0.07190.10010.7766-0.08040.647242.2992-15.5606-2.4397
201.8481-0.5064-2.817.2454-5.50587.08450.03740.00770.1994-0.9753-0.21330.03480.51810.1170.08180.52110.0481-0.05130.7469-0.04420.51641.7989-29.39037.3448
214.4781-3.2251-2.93683.07662.22781.9939-0.73820.9432-0.88050.4915-0.6733-1.38840.82241.29581.20170.6695-0.0526-0.01490.92260.13610.909865.32212.508718.8042
225.1781-0.3494-0.33472.03620.58459.7049-0.1684-0.1819-0.10250.1881-0.2558-0.1463-0.32440.87430.34960.5311-0.00380.07580.52610.05530.514958.098512.832114.9752
236.94984.2325.32886.63065.43895.1842-0.1765-0.5981-1.380.87050.3591-0.68660.1416-0.2784-0.27770.59790.1037-0.01170.51210.15560.495955.88615.859220.3109
244.07462.14445.14547.50123.25876.53650.19850.9296-0.84010.2457-0.23910.63370.8493-0.72250.0990.5619-0.0190.10230.7608-0.06390.580347.63658.08859.1543
253.71614.1643.66294.70164.52244.1830.05620.37250.27-1.0595-0.28010.224-0.191-0.90290.23410.63940.1780.10250.81690.08650.539545.728120.9077.1983
268.7266-3.56796.25045.2047-3.30238.86460.0982-0.00670.4457-0.1846-0.3971-0.4492-0.85010.07050.21940.4987-0.02510.09890.5684-0.00040.540455.35519.128419.8554
279.34980.7374.34734.2649-0.08194.99380.335-0.116-0.27320.0641-0.0383-0.0870.44530.2083-0.3520.45890.020.10130.6704-0.04150.446347.835820.624627.8366
281.56430.1291.53758.29333.84583.4802-0.0713-0.04350.6387-0.0090.11980.2624-0.6362-0.3682-0.02870.60350.03640.05290.63040.02770.679145.072632.960823.3306
292.62221.6675-0.89554.0422-3.65943.922-0.1713-0.0220.6870.2005-0.2374-0.0024-0.9321-0.42860.41410.8794-0.0155-0.01130.8032-0.13870.642146.699139.478136.5206
300.84471.39460.03676.51753.71734.32310.36470.1810.19360.31720.0456-0.5287-0.05620.6764-0.38290.4255-0.03410.03140.6818-0.05890.560650.452224.618128.7116
315.3318-0.26574.96977.5829-5.18887.6404-0.0466-0.44310.26720.0823-0.00420.1332-0.3127-0.5360.03630.49590.13090.03930.6865-0.03960.509139.383719.147413.0266
325.42670.00333.97987.43461.38263.77920.3127-0.0622-0.37160.2265-0.42130.6841.0218-0.2610.03850.435-0.0730.02780.6610.03360.585546.06789.726422.0848
337.9644-2.4048-3.02777.67461.00774.24740.1234-0.46570.14690.367-0.4417-0.38480.1242-0.05560.27690.5961-0.03580.020.77660.05380.527745.431615.887933.1865
343.0576-5.36592.91119.9227-5.26262.91851.27630.3715-0.2674-0.7337-0.58611.40210.5976-0.2243-0.81390.59860.04110.00850.9132-0.02040.821833.472115.951727.8205
359.60246.94431.7127.37864.58064.93660.47830.4463-0.19861.11961.0317-0.7002-0.08522.02-1.35440.6482-0.0483-0.03060.8841-0.01280.639342.19.074938.3149
361.7891-0.16183.28949.4789-2.11996.40030.12320.01740.4299-0.07260.30040.2914-0.6801-0.2951-0.43360.51760.06440.10640.8899-0.05870.546935.961922.954332.0843
371.6903-1.6525-3.44321.68153.50957.1956-0.54361.3204-0.6117-0.7087-0.39281.0862-0.0071-2.58690.83791.20140.0237-0.39991.4965-0.10931.09830.043431.948528.9532
388.2206-1.4079-3.92499.5422-2.61913.31440.54970.38910.32930.5567-0.43341.5973-1.6752-0.7554-0.1820.87330.06740.16290.9335-0.180.839936.814829.129438.0456
395.5478-5.1354-0.34284.89650.17027.5413-0.0763-0.73481.23121.9249-0.9043-0.8812-1.29160.16770.7050.6424-0.15740.01760.9964-0.15490.579546.239721.128844.5063
400.7428-0.1857-1.10984.3016-4.39997.75930.2002-0.42560.1208-0.0748-0.3555-0.4328-0.11280.87980.15160.5156-0.1141-0.02380.8348-0.06720.589951.738327.335439.4728
417.97530.84292.98112.6755-3.64137.32430.475-0.69310.8010.9243-0.67630.6173-2.7112-1.57680.32020.92670.09940.19551.5459-0.2271.10088.4717.146247.1574
427.91445.84282.28664.53672.52832.1470.28520.1254-0.51320.1697-0.93871.80890.3823-0.9030.67930.5966-0.18810.04181.084-0.10270.936712.5133-3.419843.5498
434.9817-3.6991-1.28373.32231.24531.88930.01980.5988-0.4052-0.9552-0.38971.4266-0.2034-0.25880.38110.5932-0.0871-0.1210.9966-0.10540.785217.20861.496237.4217
447.52031.03944.30935.36145.84828.0652-0.28990.1984-0.3971-0.036-0.24620.45160.4275-0.22860.52130.6863-0.24270.04260.7093-0.02180.871823.1159-14.513841.6245
452.2074-3.21631.61979.2011-1.53231.69520.09410.0893-0.34410.9771-0.23610.92120.1138-0.66030.11420.5938-0.18990.10790.87190.0120.686919.6936-2.460250.2927
466.50234.2003-3.76835.18760.15264.8059-0.80970.28831.4518-0.38751.10791.7204-0.79020.2763-0.60490.67120.04210.01780.9315-0.13230.873319.61514.737647.0819
471.22962.0315-0.06246.5596-2.14091.2032-0.1372-0.0417-0.15280.27860.14960.13160.0582-0.01890.09390.5781-0.03690.04490.75970.02210.496231.20273.680750.3199
486.7308-2.4686-3.26415.68961.85818.4599-0.3061-0.6186-0.29520.09880.16840.91890.89070.02790.10780.6993-0.08920.12410.8245-0.07440.629827.5223-2.933556.2172
492.0622-1.2711-0.20678.43462.27119.39760.0561-0.9281-1.05321.61450.07870.32320.3779-0.2899-0.15321.0455-0.0440.090.7109-0.02750.658431.0877-1.259863.4529
509.59680.6913-1.67893.03963.49114.7095-0.336-0.583-0.1110.92220.1621-0.86230.19060.90760.1950.8177-0.0504-0.04660.7508-0.00820.516837.1276.286761.8845
513.68383.4704-2.38483.8114-0.4779.71760.0367-1.3128-0.52161.9511-0.1102-0.6558-0.13960.9862-0.11240.99880.0538-0.02910.7918-0.0730.651735.837512.570868.3487
523.27711.43471.75585.72970.21410.8607-0.1314-0.3699-0.11660.5671-0.10620.5350.084-0.61930.21880.4488-0.06380.05930.6395-0.03160.447227.2935.901152.4004
539.58710.07395.75039.9306-2.35984.1141-0.1894-0.11350.1790.46810.0097-0.25060.27120.60090.08690.87610.0035-0.02330.7626-0.02520.59132.9978-11.32948.1345
544.2418-2.6929-0.29662.8603-1.34872.1496-0.11730.3431-0.0307-0.6678-0.22960.55470.3051-0.43180.34990.6123-0.1086-0.00790.7374-0.07120.563426.86660.455638.3512
558.7915-6.22951.73868.0808-1.40792.31980.36310.2109-0.2988-0.4637-0.1842-0.10240.1230.3796-0.19130.512-0.12260.03060.7208-0.09440.597335.52737.421744.5421
562.92980.372-1.69241.574-2.32973.98580.47220.47290.76-0.66610.36540.9565-1.33330.1634-0.84110.9174-0.16980.07720.9703-0.03220.860733.93298.870735.3482
578.1322-0.56873.15452.5919-1.11929.64-0.0942-0.42920.57220.0058-0.0837-1.50640.27271.14690.06580.5108-0.0192-0.0140.7119-0.13940.713139.7818.951647.7307
585.87152.75212.2276.12176.99678.139-0.57151.7578-0.65880.335-1.73920.0562-2.52860.71431.94471.45250.1244-0.17331.2311-0.00931.281146.76891.15257.2369
598.2068-0.84435.596710.0645-4.79257.43240.13360.06140.2451-0.0849-0.1138-0.7792-0.48150.6536-0.03510.5785-0.140.08870.7618-0.16930.569239.198617.645352.1405
602.577-2.53141.62368.9727-3.70224.43620.0988-0.2270.2661.157-0.16590.5228-0.3354-0.03050.02950.7242-0.0850.1620.665-0.02720.60228.79316.17960.4979
610.13840.6278-1.06991.7075-3.17196.0516-0.4483-1.90221.0639-0.03080.18280.3972-0.029-1.67540.96780.79610.5838-0.05141.3706-0.35831.15719.710112.03484.0995
621.9255-2.5832-3.38144.25574.9776.19690.4280.22690.8951-0.42640.30580.0724-1.12220.035-0.18720.96430.68110.21871.54040.06061.405817.363722.1683.8059
632.25873.61891.57067.47712.5061.0634-0.2827-0.34050.60850.409-0.1070.7464-0.2017-0.44310.36170.6830.3438-0.09231.3027-0.2341.16711.53618.38972.0801
648.04165.1687-0.48953.9088-0.57743.75150.2477-0.9160.91530.8851-0.41081.8824-0.4724-1.36450.17230.61380.2508-0.0181.3129-0.25980.84918.02149.9969.7058
650.67180.12370.43150.7786-0.60290.79830.8249-0.31441.9621-1.1534-1.5314-1.9241-1.355-0.88180.49430.96410.39390.03370.8838-0.1531.022527.283222.5326.345
668.85882.93912.56917.7781-0.1895.53870.273-0.24640.8657-0.5873-0.46121.0491-1.9897-1.40270.11310.83040.6564-0.06171.019-0.1210.772825.261819.6613-3.2961
672.6848-0.91190.12054.3555-0.48941.98250.1938-0.32310.1881-0.5788-0.62680.9151-0.3076-0.79350.40390.47390.2083-0.11980.901-0.18430.639521.32961.3192-2.4409
687.38554.73-1.54765.69612.10133.0299-0.6455-0.12810.3252-1.1207-0.01350.836-0.5530.00680.6420.75750.278-0.2120.80780.01770.631828.377610.517-10.6387
695.01651.4601-0.31617.48880.23124.3721-0.31610.38870.5607-1.4338-0.24090.3758-1.27630.23330.51010.94310.03-0.20860.750.04290.582532.3022.4424-17.8547
704.0808-2.9143-2.01544.133-1.80547.857-0.19290.54570.0481-1.8495-0.3648-0.6140.02551.09310.38821.06330.062-0.06470.7721-0.03450.645430.0553-8.3214-22.6745
714.48332.5507-1.84314.06551.2112.4172-0.00420.39160.0866-0.9127-0.27820.8946-0.2098-0.88370.27580.53160.2282-0.21240.8214-0.0920.57622.8156-0.7937-11.1638
722.98561.06640.59834.7403-3.47339.70130.1819-0.29140.1661-0.3294-0.21160.7915-1.276-0.42110.04050.65650.2464-0.02720.7202-0.14430.592331.138312.8341-1.2001
734.30120.7155-4.27912.2791-0.2584.31930.61980.88390.1853-0.293-0.7207-0.0906-1.1288-1.624-0.19550.69030.0633-0.090.7501-0.17970.808936.399615.7201-1.2696
749.49637.5431-2.70967.2154-1.22862.25710.0794-0.21750.0520.6682-0.10660.1702-0.4715-0.79740.080.44670.144-0.06920.8014-0.13870.517228.565610.70457.9442
752.00640.36062.44256.83352.91693.86220.0195-0.46330.0981-0.0062-0.27950.45180.1308-0.56830.230.34460.0996-0.02610.7272-0.04360.464428.8673-2.63042.0079
769.8275-3.061-6.36527.6701-0.60675.177-0.3746-0.4223-1.70050.1385-0.53750.69420.56250.17390.8440.5318-0.04480.03010.70050.00790.776834.7378-0.06237.482
776.00784.99120.23887.0001-1.63314.92620.3533-0.0739-0.01570.0045-0.34560.0152-0.19560.2071-0.12320.46430.15690.05180.5740.00340.549836.7245-3.286-4.2021
785.37934.1112-3.77144.1935-2.71762.80861.6598-0.10021.4707-1.3316-1.3145-0.1155-0.58071.289-0.2980.75810.18960.1030.818-0.00641.272942.8862-4.4702-12.3337
792.18872.3862-4.24533.1801-5.46799.9979-0.7872-0.4507-0.8123-1.39750.0482-1.2530.7839-0.23020.73960.53550.0738-0.0230.65280.02540.753132.9526-12.2603-8.6841
802.03110.1490.57048.3251-2.8383.5660.19630.1942-0.1418-1.11660.33450.97840.6754-0.6215-0.56240.54660.1028-0.19070.7118-0.08580.571723.7346-11.8546-9.9909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:7)A0 - 7
2X-RAY DIFFRACTION2(chain A and resid 8:19)A8 - 19
3X-RAY DIFFRACTION3(chain A and resid 20:25)A20 - 25
4X-RAY DIFFRACTION4(chain A and resid 26:36)A26 - 36
5X-RAY DIFFRACTION5(chain A and resid 37:49)A37 - 49
6X-RAY DIFFRACTION6(chain A and resid 50:57)A50 - 57
7X-RAY DIFFRACTION7(chain A and resid 58:71)A58 - 71
8X-RAY DIFFRACTION8(chain A and resid 72:96)A72 - 96
9X-RAY DIFFRACTION9(chain A and resid 97:109)A97 - 109
10X-RAY DIFFRACTION10(chain A and resid 110:126)A110 - 126
11X-RAY DIFFRACTION11(chain A and resid 127:143)A127 - 143
12X-RAY DIFFRACTION12(chain A and resid 144:156)A144 - 156
13X-RAY DIFFRACTION13(chain A and resid 157:167)A157 - 167
14X-RAY DIFFRACTION14(chain A and resid 168:175)A168 - 175
15X-RAY DIFFRACTION15(chain A and resid 176:183)A176 - 183
16X-RAY DIFFRACTION16(chain A and resid 184:188)A184 - 188
17X-RAY DIFFRACTION17(chain A and resid 189:193)A189 - 193
18X-RAY DIFFRACTION18(chain A and resid 194:201)A194 - 201
19X-RAY DIFFRACTION19(chain A and resid 202:206)A202 - 206
20X-RAY DIFFRACTION20(chain A and resid 207:218)A207 - 218
21X-RAY DIFFRACTION21(chain C and resid 0:4)C0 - 4
22X-RAY DIFFRACTION22(chain C and resid 5:19)C5 - 19
23X-RAY DIFFRACTION23(chain C and resid 20:26)C20 - 26
24X-RAY DIFFRACTION24(chain C and resid 27:36)C27 - 36
25X-RAY DIFFRACTION25(chain C and resid 37:46)C37 - 46
26X-RAY DIFFRACTION26(chain C and resid 47:57)C47 - 57
27X-RAY DIFFRACTION27(chain C and resid 58:71)C58 - 71
28X-RAY DIFFRACTION28(chain C and resid 72:95)C72 - 95
29X-RAY DIFFRACTION29(chain C and resid 96:106)C96 - 106
30X-RAY DIFFRACTION30(chain C and resid 107:121)C107 - 121
31X-RAY DIFFRACTION31(chain C and resid 122:136)C122 - 136
32X-RAY DIFFRACTION32(chain C and resid 137:148)C137 - 148
33X-RAY DIFFRACTION33(chain C and resid 149:159)C149 - 159
34X-RAY DIFFRACTION34(chain C and resid 160:167)C160 - 167
35X-RAY DIFFRACTION35(chain C and resid 168:175)C168 - 175
36X-RAY DIFFRACTION36(chain C and resid 176:182)C176 - 182
37X-RAY DIFFRACTION37(chain C and resid 183:187)C183 - 187
38X-RAY DIFFRACTION38(chain C and resid 188:197)C188 - 197
39X-RAY DIFFRACTION39(chain C and resid 198:203)C198 - 203
40X-RAY DIFFRACTION40(chain C and resid 204:218)C204 - 218
41X-RAY DIFFRACTION41(chain D and resid -1:3)D-1 - 3
42X-RAY DIFFRACTION42(chain D and resid 4:17)D4 - 17
43X-RAY DIFFRACTION43(chain D and resid 18:30)D18 - 30
44X-RAY DIFFRACTION44(chain D and resid 31:42)D31 - 42
45X-RAY DIFFRACTION45(chain D and resid 43:55)D43 - 55
46X-RAY DIFFRACTION46(chain D and resid 56:60)D56 - 60
47X-RAY DIFFRACTION47(chain D and resid 61:71)D61 - 71
48X-RAY DIFFRACTION48(chain D and resid 72:79)D72 - 79
49X-RAY DIFFRACTION49(chain D and resid 80:87)D80 - 87
50X-RAY DIFFRACTION50(chain D and resid 88:96)D88 - 96
51X-RAY DIFFRACTION51(chain D and resid 97:106)D97 - 106
52X-RAY DIFFRACTION52(chain D and resid 107:124)D107 - 124
53X-RAY DIFFRACTION53(chain D and resid 125:133)D125 - 133
54X-RAY DIFFRACTION54(chain D and resid 134:149)D134 - 149
55X-RAY DIFFRACTION55(chain D and resid 150:165)D150 - 165
56X-RAY DIFFRACTION56(chain D and resid 166:173)D166 - 173
57X-RAY DIFFRACTION57(chain D and resid 174:182)D174 - 182
58X-RAY DIFFRACTION58(chain D and resid 183:187)D183 - 187
59X-RAY DIFFRACTION59(chain D and resid 188:206)D188 - 206
60X-RAY DIFFRACTION60(chain D and resid 207:218)D207 - 218
61X-RAY DIFFRACTION61(chain B and resid 1:6)B1 - 6
62X-RAY DIFFRACTION62(chain B and resid 7:11)B7 - 11
63X-RAY DIFFRACTION63(chain B and resid 12:17)B12 - 17
64X-RAY DIFFRACTION64(chain B and resid 18:32)B18 - 32
65X-RAY DIFFRACTION65(chain B and resid 33:38)B33 - 38
66X-RAY DIFFRACTION66(chain B and resid 39:49)B39 - 49
67X-RAY DIFFRACTION67(chain B and resid 50:68)B50 - 68
68X-RAY DIFFRACTION68(chain B and resid 69:81)B69 - 81
69X-RAY DIFFRACTION69(chain B and resid 82:96)B82 - 96
70X-RAY DIFFRACTION70(chain B and resid 97:105)B97 - 105
71X-RAY DIFFRACTION71(chain B and resid 106:119)B106 - 119
72X-RAY DIFFRACTION72(chain B and resid 120:128)B120 - 128
73X-RAY DIFFRACTION73(chain B and resid 129:133)B129 - 133
74X-RAY DIFFRACTION74(chain B and resid 134:144)B134 - 144
75X-RAY DIFFRACTION75(chain B and resid 145:162)B145 - 162
76X-RAY DIFFRACTION76(chain B and resid 163:171)B163 - 171
77X-RAY DIFFRACTION77(chain B and resid 172:185)B172 - 185
78X-RAY DIFFRACTION78(chain B and resid 186:192)B186 - 192
79X-RAY DIFFRACTION79(chain B and resid 193:199)B193 - 199
80X-RAY DIFFRACTION80(chain B and resid 200:218)B200 - 218

+
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