[English] 日本語
Yorodumi
- PDB-3ty6: ATP-dependent Protease HslV from Bacillus anthracis str. Ames -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ty6
TitleATP-dependent Protease HslV from Bacillus anthracis str. Ames
ComponentsATP-dependent protease subunit HslV
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-beta-alpha sandwich / peotease / cytosol
Function / homology
Function and homology information


HslU-HslV peptidase / HslUV protease complex / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / metal ion binding
Similarity search - Function
ATP-dependent protease, HslV subunit / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent protease subunit HslV
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsKim, Y. / Mulligan, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: ATP-dependent Protease HslV from Bacillus anthracis str. Ames
Authors: Kim, Y. / Mulligan, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Advisory / Database references / Category: citation_author / pdbx_unobs_or_zero_occ_atoms / Item: _citation_author.name
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease subunit HslV
F: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,04512
Polymers118,4686
Non-polymers5766
Water1,09961
1
A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease subunit HslV
F: ATP-dependent protease subunit HslV
hetero molecules

A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease subunit HslV
F: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,08924
Polymers236,93612
Non-polymers1,15312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area35470 Å2
ΔGint-383 kcal/mol
Surface area73180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.255, 127.543, 90.100
Angle α, β, γ (deg.)90.00, 130.03, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
ATP-dependent protease subunit HslV


Mass: 19744.691 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS3681, BA_3968, GBAA_3968, hslV / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81WK5, HslU-HslV peptidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 2.5 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 21, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 41877 / Num. obs: 41877 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 73.67 Å2 / Rsym value: 0.053 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2038 / Rsym value: 0.744 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: dev_851)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 2Z3B
Resolution: 2.498→41.076 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.26 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2114 5.05 %random
Rwork0.165 ---
all0.166 41861 --
obs0.166 41861 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 93.909 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 86 Å2
Baniso -1Baniso -2Baniso -3
1--14.8826 Å2-0 Å2-3.9106 Å2
2--11.6083 Å20 Å2
3---3.2743 Å2
Refinement stepCycle: LAST / Resolution: 2.498→41.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8063 0 30 61 8154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078200
X-RAY DIFFRACTIONf_angle_d1.10111031
X-RAY DIFFRACTIONf_dihedral_angle_d15.4042958
X-RAY DIFFRACTIONf_chiral_restr0.0851252
X-RAY DIFFRACTIONf_plane_restr0.0041418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4987-2.55680.40321430.34852639278294
2.5568-2.62060.3431240.32562604272895
2.6206-2.69130.36471220.31782689281196
2.6913-2.77030.34711420.3012606274895
2.7703-2.85950.3521450.30452650279595
2.8595-2.96140.32241460.28372662280895
2.9614-3.07950.29631380.26922637277595
3.0795-3.21920.30681350.25112630276595
3.2192-3.38820.25431440.2152697284195
3.3882-3.59930.25021580.19192594275294
3.5993-3.87550.21211580.16442647280594
3.8755-4.26220.16511460.13712637278394
4.2622-4.87160.13181280.10172651277995
4.8716-6.10980.15221390.12052669280895
6.1098-20.31540.14461400.09862684282494
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)
11.8364-0.95890.31711.5162-0.76656.73560.04360.34830.0125-0.14790.1955-0.06940.09740.02860.7041.0267-0.0628-0.01260.46870.08950.234926.0531-18.7067-22.0512
24.89912.2658-0.70242.021-1.23722.03290.3176-0.5349-0.16010.1712-0.035-0.26870.21290.0412-0.24370.8387-0.1575-0.13030.3168-0.09660.193631.3619-18.0438-17.4962
36.92461.0459-4.36317.5838-4.55727.5731.197-0.8343-0.24580.4931-0.62-0.1875-0.9548-0.967-0.45170.9622-0.009-0.05850.79340.26720.353215.5844-24.8256-9.752
44.15180.75422.71074.6120.67481.7947-0.1882-0.85130.07860.3606-0.2486-0.0951-0.0765-0.47130.46830.7872-0.1231-0.10730.67680.10850.234815.5802-15.097-11.2081
56.85661.38881.14258.4125-2.74693.58170.5037-0.565-0.32820.3108-0.61550.14580.5957-0.43030.03750.7705-0.1876-0.15160.80220.11860.27646.0937-14.0013-16.7832
62.4994-2.352-2.2574.373.83634.23240.0826-0.26130.2828-1.77890.95050.2515-1.1239-0.3346-0.90.9976-0.0884-0.08360.63620.19840.376616.5606-7.6738-18.106
72.1679-0.8875-0.66161.8257-0.00721.77670.28470.3832-0.1124-0.5685-0.32880.1687-0.04-0.1119-0.01530.8534-0.077-0.19290.66250.16970.296314.7204-19.5314-24.9716
87.87191.5156-0.69826.56760.20048.4253-0.29320.0063-0.84830.15620.43230.0511.04420.2797-0.23180.81080.0271-0.03230.4402-0.02030.170327.6616-28.7161-29.7091
98.61895.644-6.21885.7659-4.82775.00970.762-0.26870.20980.1781-0.46370.48150.01830.63910.01190.8994-0.1201-0.18740.50350.20110.468131.5361-22.7543-19.8224
107.94230.83784.80113.357-0.89465.9971-0.04080.4391-0.01060.32410.2261-0.144-0.6851.2268-0.08910.8813-0.1852-0.07440.6323-0.05820.22643.231-8.0065-40.1783
112.47341.2664-1.80512.8942-0.58911.3668-0.2866-0.4257-0.6178-0.14870.49960.33940.6325-0.41550.10860.7326-0.1017-0.1060.39050.19790.2050.7986-12.1084-40.7033
126.63430.3926-3.98271.7859-0.11862.57560.2416-0.07420.2589-0.3360.10050.0201-0.1692-0.3012-0.27550.82910.0788-0.00510.44140.16690.227611.876-15.662-34.5942
132.97913.44572.1375.49650.56243.9454-0.3867-0.9142-0.81331.50780.59250.7812.4937-1.13680.00761.51430.01410.43270.82810.17130.9446-11.0539-10.9886-30.4974
147.38350.69445.04153.1558-0.71887.23580.0251-1.5722-0.14080.44460.27150.3604-0.7324-1.2604-0.13340.777-0.0974-0.04570.83670.17760.2407-4.1097-4.7901-26.9073
155.79255.81291.09997.52812.89165.13920.90.20522.83351.6233-0.38310.67241.1723-0.1851-0.45011.06130.30050.14030.81140.03980.8068-8.86565.3635-28.6523
168.6389-2.25281.28361.3749-1.27062.7320.030.08911.00670.46060.19430.16630.2896-0.3207-0.17950.6898-0.0864-0.01350.43250.15730.4344-1.47530.6355-32.578
175.569-2.07512.76993.45882.00946.281-0.68610.0130.3634-0.15851.1460.3964-0.5382-0.4185-0.03750.7089-0.1754-0.0350.61350.23230.4846-1.70841.9582-40.8435
185.8925-1.97080.02565.83171.166.4723-0.29570.88610.1754-0.9971-0.19350.65730.3758-0.46690.68190.6144-0.1587-0.10340.44530.08820.271-2.3124-6.8301-54.0236
192.00013.66845.23095.86862.27918.496-0.76140.4735-1.52720.13040.9853-0.09991.97730.0368-0.1640.9861-0.0110.00640.39790.04010.3671.6021-13.9426-49.1511
205.16851.322-3.78682.72051.01864.429-0.8892-0.1253-0.85440.22750.89380.53070.9897-0.37891.2310.9313-0.1039-0.02380.63960.3430.48723.3604-14.9911-41.9117
214.46630.2123-2.7931.86711.21112.8321-0.3293-0.4092-0.16960.11520.60320.43560.3989-1.0984-0.37570.7817-0.137-0.03860.82310.15930.1756-3.475723.886-46.5976
227.1696-4.2325-6.19017.04432.11495.8654-1.4320.51310.8672-0.2080.5350.25031.5389-0.31060.18731.3654-0.1652-0.39970.47860.01480.6474-0.43949.4584-45.7892
239.8749-0.943-4.30573.27872.91963.856-0.4701-2.2808-0.35790.9463-0.26842.11110.8724-2.06750.5760.65070.01970.01471.54230.08910.968-15.696425.5186-36.9322
241.7204-1.05072.40937.7683.02956.2130.566-0.5014-0.46641.1871-0.86150.98870.9591-1.52980.49931.0122-0.42260.01130.9809-0.07520.3375-8.014322.2511-31.2334
255.43-2.23812.57482.1549-2.6495.64630.5115-1.71830.22670.12530.31270.32210.8762-1.9998-0.7180.9245-0.3940.06121.0991-0.05050.4568-4.698931.5535-26.3328
266.0131-4.34290.24133.86980.13384.31460.4903-0.7150.56710.2257-0.3977-0.64110.45280.4288-0.12790.6321-0.1433-0.04510.48710.0340.2382.005921.8705-30.2927
273.7019-0.45670.59883.96010.30176.7783-0.04610.01760.4136-0.217-0.52080.0636-0.91090.4430.50750.69450.0306-0.04660.40330.01720.1849-0.60832.4065-38.6874
283.24630.00450.94566.9529-1.09726.1793-0.04080.01940.0997-0.84960.11390.11110.1298-1.19810.00590.67-0.0197-0.08230.53410.20160.2224-0.869930.4193-54.8896
293.752-0.6037-0.34182.64171.36196.7787-0.17561.07890.2036-0.06530.20060.12380.3766-1.77470.02160.9011-0.3969-0.19510.96110.31560.4851-3.786119.3414-49.9667
306.87-2.15672.15512.9352-2.41446.61460.020.44070.2034-0.7201-0.25550.03271.09921.08240.17190.9035-0.04130.0660.77390.05690.359440.652242.6646-39.5472
315.3284-3.71843.20044.5089-5.97659.3199-0.4693-0.70230.5514-0.3350.4167-0.27140.16750.1277-0.16150.5381-0.1506-0.07320.7797-0.03560.486346.156442.0959-34.8749
326.669-3.72392.36123.8514-3.48063.6412-0.40840.96731.2718-0.80670.4356-0.93290.9717-0.17940.06690.7144-0.1301-0.0960.81060.29680.671251.270848.8023-51.9588
335.0954-1.41744.21828.0584-3.16044.1061-0.15550.6684-0.09470.2467-0.0848-0.1026-0.70310.84240.14880.461-0.0591-0.04120.56050.22330.367149.59439.1119-51.7352
345.7982.03442.5466.2206-2.33323.0079-0.79921.60720.3241-0.46341.34740.0532-0.3081-0.4737-0.46320.696-0.092-0.07120.91340.09470.292942.607738.0186-60.1158
353.6187-1.18530.01979.4916-2.7255.81080.44540.2502-0.36710.0525-0.14190.18580.6285-0.022-0.34310.5558-0.1391-0.18750.67790.05320.319241.532637.3415-50.8633
363.1988-2.1625-0.92944.87733.5993.2790.10940.56420.3566-0.074-0.1460.23490.10310.1417-0.04770.717-0.0341-0.02520.46830.19450.282534.346341.3784-48.472
379.08521.4718-0.74348.86080.56899.0883-0.095-1.0761-0.28550.2315-0.838-0.3855-1.0606-0.76710.88410.65610.0151-0.15810.78870.06810.506530.279753.5061-38.8515
384.8789-2.25660.21725.5463-1.30345.13780.2661-0.9885-0.27890.880.6355-0.2714-0.56560.0832-0.55070.7186-0.0434-0.18550.7349-0.02210.346738.147251.5805-33.7611
395.90481.196-0.36844.0156-3.27372.7734-0.0982-0.44710.27310.7010.3167-0.2703-0.71170.8744-0.3780.81070.0669-0.1130.8115-0.14180.47243.990446.7719-34.5524
402.2042-0.3590.99073.42752.24354.61750.2336-0.06560.1504-0.09460.4708-0.0189-0.06760.106-0.56260.7398-0.15980.01170.51460.18160.284316.742733.2271-62.4712
416.47241.36181.58454.41662.42412.2980.0571-0.42431.3022-0.1879-0.3732-0.00370.0838-0.21290.3410.424-0.10490.00120.52560.04530.540126.321337.8968-58.0636
425.49791.31986.09644.9367-0.24617.39230.27570.94470.2644-1.0444-0.3067-0.9427-0.82710.6577-0.03190.66840.05890.06460.91850.0760.336630.41628.509-69.5274
435.67270.5321.16213.72620.43184.38930.720.5228-0.843-0.0801-0.1357-0.52150.65820.5466-0.3530.6652-0.0391-0.19540.47520.07010.200524.034821.5881-66.6908
443.87920.6257-1.04142.15510.12583.06890.09540.12310.2179-0.233-0.145-0.167-0.5437-0.1568-0.99150.724-0.1435-0.08970.68510.32590.29114.302230.9155-61.7404
453.1799-1.07125.42756.0272-1.85239.4759-0.08270.15041.60290.1816-0.73380.4588-0.79290.08530.81670.7687-0.07220.03120.58590.09690.56539.859937.9113-58.8639
466.5763-0.175-4.1544.82622.24043.56430.8680.03221.1978-0.09990.27030.0098-1.12170.338-0.60120.6910.0003-0.10530.35970.01980.590217.25138.9759-58.3807
475.77253.9428-0.77464.2660.17130.54060.0617-0.41971.01440.5072-0.64710.32340.35820.00020.58870.8085-0.2496-0.21270.74330.03840.522913.75011.229-61.6611
485.10780.4936-1.09938.94471.7862.25390.57580.35510.8218-0.0875-0.56580.11410.06740.61620.1250.6606-0.1544-0.06920.76380.09730.34511.65588.0434-63.4739
494.1182.2203-4.86917.1834-0.55946.4708-0.76491.38020.6208-1.3671-0.1986-0.5765-0.95411.23370.80431.0313-0.2828-0.26471.29390.43640.650619.0949-1.5292-77.9245
503.6558-0.70122.34461.9184-0.48731.5172-0.46580.9468-0.3815-0.8569-0.2627-0.16270.5357-0.49270.68861.1403-0.15880.1431.0158-0.04180.301325.89611.7566-71.3544
516.4287-1.3362-1.17266.75711.26826.86740.23380.9731-0.7225-0.5466-0.2068-1.33581.34920.03890.24460.86470.1060.23250.4814-0.06510.704931.2346-7.4053-68.853
529.29044.40531.278.45240.55587.3963-0.70040.8870.9374-0.16480.7579-0.1894-0.16950.6203-0.06360.6540.0378-0.12080.76340.12970.533528.38132.176-61.7773
536.24620.0061-3.20153.88390.10475.87920.00250.7443-0.3149-0.0890.0363-0.3951.7386-0.1944-0.00180.92190.0315-0.16150.55670.00380.346219.772-8.3273-62.8686
549.4422-1.556-4.03437.9851-2.83743.3108-0.4127-0.5101-0.8703-0.081-0.20450.030.6222-1.00830.64110.7538-0.0602-0.08320.6823-0.01260.33454.0319-10.3398-59.304
551.4952-2.1628-1.80367.85985.07736.8506-0.42240.97910.2690.1603-0.51770.76850.3454-1.29780.68760.5934-0.2981-0.08020.7350.1930.55983.1976-0.949-61.7927
567.6517-6.073-7.58094.85776.12327.8130.63171.40840.6884-0.6473-0.8607-0.1833-0.5597-1.5297-0.17110.8717-0.0414-0.00920.57970.12480.46878.02244.7096-64.1219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:13)
2X-RAY DIFFRACTION2chain 'A' and (resseq 14:39)
3X-RAY DIFFRACTION3chain 'A' and (resseq 40:47)
4X-RAY DIFFRACTION4chain 'A' and (resseq 48:72)
5X-RAY DIFFRACTION5chain 'A' and (resseq 73:90)
6X-RAY DIFFRACTION6chain 'A' and (resseq 91:104)
7X-RAY DIFFRACTION7chain 'A' and (resseq 105:131)
8X-RAY DIFFRACTION8chain 'A' and (resseq 132:166)
9X-RAY DIFFRACTION9chain 'A' and (resseq 167:179)
10X-RAY DIFFRACTION10chain 'B' and (resseq 2:13)
11X-RAY DIFFRACTION11chain 'B' and (resseq 14:27)
12X-RAY DIFFRACTION12chain 'B' and (resseq 28:39)
13X-RAY DIFFRACTION13chain 'B' and (resseq 40:47)
14X-RAY DIFFRACTION14chain 'B' and (resseq 48:72)
15X-RAY DIFFRACTION15chain 'B' and (resseq 73:90)
16X-RAY DIFFRACTION16chain 'B' and (resseq 91:112)
17X-RAY DIFFRACTION17chain 'B' and (resseq 113:131)
18X-RAY DIFFRACTION18chain 'B' and (resseq 132:151)
19X-RAY DIFFRACTION19chain 'B' and (resseq 152:166)
20X-RAY DIFFRACTION20chain 'B' and (resseq 167:179)
21X-RAY DIFFRACTION21chain 'C' and (resseq 4:27)
22X-RAY DIFFRACTION22chain 'C' and (resseq 28:39)
23X-RAY DIFFRACTION23chain 'C' and (resseq 40:47)
24X-RAY DIFFRACTION24chain 'C' and (resseq 48:72)
25X-RAY DIFFRACTION25chain 'C' and (resseq 73:90)
26X-RAY DIFFRACTION26chain 'C' and (resseq 91:104)
27X-RAY DIFFRACTION27chain 'C' and (resseq 105:131)
28X-RAY DIFFRACTION28chain 'C' and (resseq 132:166)
29X-RAY DIFFRACTION29chain 'C' and (resseq 167:179)
30X-RAY DIFFRACTION30chain 'F' and (resseq 1:13)
31X-RAY DIFFRACTION31chain 'F' and (resseq 14:39)
32X-RAY DIFFRACTION32chain 'F' and (resseq 40:47)
33X-RAY DIFFRACTION33chain 'F' and (resseq 48:72)
34X-RAY DIFFRACTION34chain 'F' and (resseq 73:90)
35X-RAY DIFFRACTION35chain 'F' and (resseq 91:112)
36X-RAY DIFFRACTION36chain 'F' and (resseq 113:131)
37X-RAY DIFFRACTION37chain 'F' and (resseq 132:151)
38X-RAY DIFFRACTION38chain 'F' and (resseq 152:166)
39X-RAY DIFFRACTION39chain 'F' and (resseq 167:179)
40X-RAY DIFFRACTION40chain 'E' and (resseq 2:22)
41X-RAY DIFFRACTION41chain 'E' and (resseq 23:46)
42X-RAY DIFFRACTION42chain 'E' and (resseq 47:73)
43X-RAY DIFFRACTION43chain 'E' and (resseq 74:131)
44X-RAY DIFFRACTION44chain 'E' and (resseq 132:151)
45X-RAY DIFFRACTION45chain 'E' and (resseq 152:166)
46X-RAY DIFFRACTION46chain 'E' and (resseq 167:179)
47X-RAY DIFFRACTION47chain 'D' and (resseq 2:13)
48X-RAY DIFFRACTION48chain 'D' and (resseq 14:39)
49X-RAY DIFFRACTION49chain 'D' and (resseq 40:47)
50X-RAY DIFFRACTION50chain 'D' and (resseq 48:72)
51X-RAY DIFFRACTION51chain 'D' and (resseq 73:90)
52X-RAY DIFFRACTION52chain 'D' and (resseq 91:104)
53X-RAY DIFFRACTION53chain 'D' and (resseq 105:131)
54X-RAY DIFFRACTION54chain 'D' and (resseq 132:151)
55X-RAY DIFFRACTION55chain 'D' and (resseq 152:166)
56X-RAY DIFFRACTION56chain 'D' and (resseq 167:179)

+
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://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