[English] 日本語
Yorodumi
- PDB-8riu: Crystal structure of the F420-reducing carbon monoxide dehydrogen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8riu
TitleCrystal structure of the F420-reducing carbon monoxide dehydrogenase component from the ethanotroph Candidatus Ethanoperedens thermophilum
Components
  • (Acetyl-CoA decarbonylase/synthase complex subunit ...) x 2
  • Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
KeywordsOXIDOREDUCTASE / Carbon monoxide dehydrogenase / F420-reductase / acetyl-coenzyme A synthase-decarbonylase complex / anaerobic oxidoreductase / CO2-releasing enzyme / C-cluster / CO / CO2 / gas channelling.
Function / homology
Function and homology information


methanogenesis, from acetate / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / methanogenesis / acetyl-CoA metabolic process / iron-sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase ...Acetyl-CoA decarbonylase/synthase complex subunit alpha / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / DHS-like NAD/FAD-binding domain superfamily / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Acetyl-CoA decarbonylase/synthase complex subunit alpha / Acetyl-CoA decarbonylase/synthase complex subunit epsilon / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
Similarity search - Component
Biological speciesCandidatus Methanoperedenaceae archaeon GB50 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsLemaire, O.N. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)WA 4053/2-1 Germany
CitationJournal: To Be Published
Title: F420 reduction as a cellular driver for anaerobic ethanotrophy
Authors: Lemaire, O.N. / Wegener, G. / Wagner, T.
History
DepositionDec 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-CoA decarbonylase/synthase complex subunit alpha
B: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
C: Acetyl-CoA decarbonylase/synthase complex subunit epsilon
D: Acetyl-CoA decarbonylase/synthase complex subunit alpha
E: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
F: Acetyl-CoA decarbonylase/synthase complex subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,17153
Polymers294,6766
Non-polymers9,49547
Water25,5451418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43020 Å2
ΔGint-468 kcal/mol
Surface area76710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.070, 159.213, 191.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Acetyl-CoA decarbonylase/synthase complex subunit ... , 2 types, 4 molecules ADCF

#1: Protein Acetyl-CoA decarbonylase/synthase complex subunit alpha / ACDS complex subunit alpha / ACDS complex carbon monoxide dehydrogenase subunit alpha / ACDS CODH ...ACDS complex subunit alpha / ACDS complex carbon monoxide dehydrogenase subunit alpha / ACDS CODH subunit alpha


Mass: 87549.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Ligands SF4, XCC and GOL are not part of the protein sequence
Source: (natural) Candidatus Methanoperedenaceae archaeon GB50 (archaea)
References: UniProt: A0A7R9N4A5, anaerobic carbon monoxide dehydrogenase
#3: Protein Acetyl-CoA decarbonylase/synthase complex subunit epsilon / ACDS complex subunit epsilon / ACDS complex carbon monoxide dehydrogenase subunit epsilon / ACDS ...ACDS complex subunit epsilon / ACDS complex carbon monoxide dehydrogenase subunit epsilon / ACDS CODH subunit epsilon


Mass: 19057.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Ligand GOL is not part of the protein sequence
Source: (natural) Candidatus Methanoperedenaceae archaeon GB50 (archaea)
References: UniProt: A0A7R9N5A2

-
Protein , 1 types, 2 molecules BE

#2: Protein Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus


Mass: 40730.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Ligands SF4, FAD and GOL are not part of the protein sequence
Source: (natural) Candidatus Methanoperedenaceae archaeon GB50 (archaea)
References: UniProt: A0A7R9R773

-
Non-polymers , 9 types, 1465 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#10: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#11: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1418 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.1 % / Description: Brown thick square plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Crystallisation was performed anaerobically at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a Coy tent containing a ...Details: Crystallisation was performed anaerobically at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a Coy tent containing a N2/H2 (97:3%) atmosphere. The reservoir chamber was filled with 90 ul of crystallisation condition and the drop was formed by spotting 0.6 ul protein with 0.6 ul of 20% (w/v) PEG 6,000; 100 mM MES pH6 and 200 mM Ammonium chloride. The protein was crystallized at 13.0 mg/ml in 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 1 mM flavin adenine dinucleotide and 1 mM Flavin mononuleotide and 10% (v/v) glycerol. Crystals were cryo-protected by soaking in 20% (w/v) PEG 6,000; 100 mM MES pH6 and 200 mM Ammonium chloride supplemented with 30% v/v glycerol for a few seconds.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.89→122.41 Å / Num. obs: 164775 / % possible obs: 95.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.042 / Rrim(I) all: 0.155 / Net I/σ(I): 10.8
Reflection shellResolution: 1.89→2.1 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.583 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8240 / CC1/2: 0.639 / Rpim(I) all: 0.46 / Rrim(I) all: 1.65 / % possible all: 73.6

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.89→39.8 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39 / Stereochemistry target values: ML
Details: The last refinement steps were performed by refining with a translation libration screw (TLS) and with modelled hydrogens in the riding position. Hydrogens were omitted in the final deposited models.
RfactorNum. reflection% reflection
Rfree0.1873 8278 5.03 %
Rwork0.1651 --
obs0.1662 164728 69.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.12 Å2
Refinement stepCycle: LAST / Resolution: 1.89→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20332 0 128 1418 21878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.233
X-RAY DIFFRACTIONf_dihedral_angle_d14.3147894
X-RAY DIFFRACTIONf_chiral_restr0.2613215
X-RAY DIFFRACTIONf_plane_restr0.0093606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.910.401230.2302121X-RAY DIFFRACTION2
1.91-1.940.2429150.2836320X-RAY DIFFRACTION4
1.94-1.960.2889300.2755575X-RAY DIFFRACTION8
1.96-1.990.2871380.2686858X-RAY DIFFRACTION12
1.99-2.010.2861550.26011068X-RAY DIFFRACTION14
2.01-2.040.2278720.24921237X-RAY DIFFRACTION17
2.04-2.070.2739860.24531493X-RAY DIFFRACTION20
2.07-2.10.2865850.24281830X-RAY DIFFRACTION25
2.1-2.130.26611260.23292248X-RAY DIFFRACTION31
2.13-2.170.25411750.22983076X-RAY DIFFRACTION42
2.17-2.20.242190.22574118X-RAY DIFFRACTION56
2.2-2.240.24962590.21645270X-RAY DIFFRACTION71
2.24-2.290.25044020.22216819X-RAY DIFFRACTION93
2.29-2.330.2593850.21347387X-RAY DIFFRACTION100
2.33-2.380.26763650.20247438X-RAY DIFFRACTION100
2.38-2.440.24154090.19547390X-RAY DIFFRACTION100
2.44-2.50.22834340.19177383X-RAY DIFFRACTION100
2.5-2.570.1914260.18727400X-RAY DIFFRACTION100
2.57-2.640.19563760.187439X-RAY DIFFRACTION100
2.64-2.730.19533990.18177423X-RAY DIFFRACTION100
2.73-2.830.20894120.17987438X-RAY DIFFRACTION100
2.83-2.940.19893910.17067468X-RAY DIFFRACTION100
2.94-3.070.19244060.16967442X-RAY DIFFRACTION100
3.07-3.240.20433810.16697491X-RAY DIFFRACTION100
3.24-3.440.17853960.16147486X-RAY DIFFRACTION100
3.44-3.70.17373820.14677546X-RAY DIFFRACTION100
3.7-4.080.16113800.13657545X-RAY DIFFRACTION100
4.08-4.670.12874190.12087559X-RAY DIFFRACTION100
4.67-5.880.15613280.14147685X-RAY DIFFRACTION100
5.88-39.80.19354240.17877897X-RAY DIFFRACTION100
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)
11.33720.4545-1.27610.9466-0.55751.8141-0.1157-0.1279-0.12410.15320.0205-0.12840.0950.10150.11380.28840.0479-0.03570.3079-0.00120.2855-0.421666.289853.1205
20.651-0.3862-0.19121.45590.20350.5927-0.0369-0.25350.0420.49130.0682-0.0618-0.0351-0.0212-0.03210.40510.0256-0.03750.3544-0.00840.2195-6.419483.423468.088
32.36480.56380.22891.6075-0.50350.53910.035-0.15280.23840.34440.00120.1035-0.2244-0.0226-0.03390.40880.05740.00980.2785-0.05060.2238-11.8062100.820559.845
41.50170.73131.51821.63581.57193.7777-0.1248-0.03290.27250.13560.01070.0534-0.4634-0.00270.11760.34210.0470.04160.2598-0.00830.259-10.3145107.731552.1919
50.70380.3624-0.44871.5424-0.95841.6179-0.0162-0.07020.01370.28120.0230.1254-0.1402-0.2264-0.02080.31080.06280.04420.3849-0.02360.2436-25.513987.96753.1551
60.96310.093-0.07781.17710.16980.5072-0.0192-0.2108-0.06620.3033-0.01650.06310.0284-0.08840.03570.34850.01490.02230.36030.00970.2141-17.086771.795662.3815
70.3439-0.19680.50571.2748-0.55151.34130.02090.0495-0.14140.19730.0060.2250.0916-0.1593-0.03460.34250.0170.08260.41060.01270.3417-27.338460.331754.7847
88.36180.21743.11021.2075-0.2372.60750.0868-0.1056-0.61270.16870.08340.28090.1511-0.1773-0.16450.33440.03570.13340.33790.01460.393-33.747150.410956.8253
92.1301-0.90452.29624.78230.0532.9876-0.12160.15160.0525-0.34090.04-0.4169-0.0312-0.09510.10250.2676-0.02380.11030.3783-0.07650.2464-2.05664.039213.2085
101.628-0.2461-0.41581.23050.67462.71990.03820.4791-0.073-0.3685-0.0306-0.14470.1396-0.0411-0.06490.3094-0.00480.09250.4233-0.04880.27881.441660.8802-0.7852
111.7516-1.6315-0.95531.74560.75044.21840.00060.6333-0.4131-0.2821-0.0182-0.42730.50880.43650.03230.52670.13050.13650.6109-0.24860.52899.956446.1612-6.1129
124.98050.51592.1261.1593-0.85572.33010.2126-0.1153-0.5485-0.06460.0390.12290.46480.0463-0.23620.5780.00270.05460.4084-0.11270.4952-1.659942.83410.0908
131.59450.410.88333.53721.16943.6130.1069-0.033-0.1366-0.02050.001-0.02770.243-0.0495-0.08510.34590.0310.11410.3917-0.06520.28761.341154.6642.1421
146.1369-1.60372.2348.5335-2.97888.41140.40181.0036-0.7671-1.29170.01660.58241.143-0.3346-0.36460.7391-0.0965-0.0180.823-0.20950.5142-15.775541.0463-9.2855
150.86270.0723-0.16342.0606-0.13672.84090.23550.6981-0.4658-0.5398-0.2168-0.12540.2334-0.1198-0.00010.54140.0790.08230.6884-0.18670.3769-1.98855.5033-12.764
162.6324-3.1369-3.62295.92395.45157.5460.13371.0608-0.0316-0.6455-0.58330.0122-0.3991-0.96760.46530.4790.0586-0.01580.6759-0.03120.2797-10.506966.4595-12.6881
170.61030.4897-0.11485.1341-1.18421.04330.00210.1161-0.2401-0.5408-0.17390.47310.38380.06670.19530.4760.05250.01340.4626-0.08120.4085-12.35583.74640.9561
180.7484-0.20660.02771.63450.8610.4911-0.00040.0724-0.07120.0448-0.0273-0.18560.1082-0.05230.0560.28970.02650.02060.3607-0.01310.2657-7.634579.585727.2366
193.0877-0.1377-1.14234.4809-2.90712.583-0.08660.8188-0.262-0.71250.08770.12030.478-0.24280.04410.3508-0.02990.0210.5396-0.1030.2817-18.504665.662216.9383
201.70511.50990.79471.87420.11411.01910.12670.22380.1627-0.0961-0.0879-0.2330.0227-0.0862-0.01680.2926-0.0110.05670.41260.00430.2331-25.090169.738829.8381
211.72540.96531.89482.11150.35742.5249-0.01770.2149-0.02520.0869-0.07670.26010.1238-0.48350.11080.2671-0.00620.04010.4677-0.03750.3558-31.374268.047330.7659
228.052-0.05815.79972.47810.20256.12670.0413-0.6177-0.3830.0666-0.05470.40190.1857-0.66830.04560.24140.00580.03220.3336-0.00890.3124-24.725163.195737.3879
239.75273.6301-2.39836.0324-4.63263.5967-0.11130.1495-0.2659-0.32090.20990.09510.3805-0.2948-0.0990.2890.02560.0550.2699-0.07780.2494-17.886854.87135.3919
241.3309-0.3015-0.35771.7531-0.28811.1218-0.0120.2183-0.0782-0.0327-0.06180.0498-0.0858-0.03960.07830.23330.00120.00110.3509-0.02470.2416-13.658972.019229.9237
253.52372.91660.38998.59661.48980.2655-0.12920.31410.3031-0.6021-0.01610.3417-0.1445-0.08610.14510.3070.007-0.040.4469-0.01120.2514-25.259977.973419.1021
260.7137-0.21410.09831.1038-0.10820.496-0.0613-0.1779-0.10380.30050.053-0.36130.01920.08620.00160.29010.0229-0.10140.31240.00390.353818.646374.857.1086
270.5210.0544-0.03741.4284-1.2222.4915-0.0613-0.0406-0.21220.04360.0583-0.26440.29370.0140.02140.26520.0409-0.03630.3208-0.00780.474617.175552.460144.2536
280.54590.21390.06560.88010.1020.4047-0.0237-0.01990.02910.14090.0255-0.4583-0.0410.1881-0.0170.23180.0082-0.07810.3507-0.01550.517631.472584.83345.2976
294.03171.1332-3.8292.0181-1.0736.9010.2059-0.12220.2976-0.00050.0914-0.4739-0.30960.5274-0.32690.3198-0.0319-0.06470.3558-0.04910.671641.2468109.59943.2151
300.9842-1.4331-0.96955.07541.17465.0239-0.0799-0.05330.0001-0.0562-0.06540.20010.0873-0.07450.15220.2515-0.0230.00320.31870.03390.2456-5.644698.678915.378
311.073-0.52390.82521.541-0.61332.2549-0.0420.12770.1078-0.2163-0.02830.056-0.1212-0.07670.07370.29190.01470.00860.35760.01690.2214-17.0287106.19524.6274
327.0003-2.5852-4.24351.9272-0.09376.48630.0496-0.4290.6476-0.2457-0.0099-0.3154-0.79580.5157-0.00850.5694-0.0789-0.06690.3007-0.05040.3384-11.119120.96275.7699
333.61630.91650.05672.6439-1.06762.3015-0.12270.43920.253-0.22150.0283-0.1856-0.32960.22870.07670.4278-0.0012-0.03740.3662-0.00680.2013-8.6826113.33391.3838
340.7655-0.1901-0.02191.7082-0.61210.9571-0.03990.20070.0414-0.45390.00030.08790.0183-0.06750.00740.50270.0219-0.03070.4149-0.03090.245-16.814105.115-7.4825
350.19570.6593-0.17662.8542-0.20320.6517-0.05610.34650.1564-0.6033-0.1679-0.5543-0.10340.00170.1890.55660.05970.08110.5130.04660.4582-2.655778.6814-1.6557
360.2294-0.60120.7491.6574-1.62842.7227-0.01660.0699-0.0140.0658-0.01220.0062-0.1965-0.03760.04660.27250.00330.0090.3172-0.01820.28785.008882.18924.5935
377.14422.27422.38928.48857.43368.6779-0.13170.79090.4784-1.01670.1857-0.1712-0.8244-0.2526-0.04120.340600.03660.39120.09270.315210.818497.036311.7698
381.4471.0247-0.3670.7218-0.38984.0426-0.02380.091-0.1898-0.18360.10020.03540.1240.0965-0.11730.2559-0.0506-0.01060.36830.0170.402522.206492.121220.5165
392.19021.31360.63732.14040.68893.1752-0.06820.4166-0.0087-0.4102-0.0086-0.4788-0.03840.64840.0310.3541-0.00450.12260.50780.04180.489925.701794.420612.9581
401.52810.02090.37851.12060.29452.17440.04890.17480.1595-0.265-0.0126-0.2969-0.23340.49270.04730.2788-0.04630.03250.37830.03270.434727.246395.997825.6078
411.38140.65550.59111.99910.55231.3075-0.06870.07910.0715-0.1395-0.0251-0.1286-0.0450.02810.09070.27490.00990.03590.35240.01340.341913.2293.574826.1477
422.73780.7552-0.49342.9453-2.14811.6694-0.240.2722-0.2512-0.79810.4602-0.31010.19670.005-0.19050.391-0.02020.10460.4319-0.0360.388417.305584.361910.3708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 257 )
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 337 )
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 417 )
5X-RAY DIFFRACTION5chain 'A' and (resid 418 through 552 )
6X-RAY DIFFRACTION6chain 'A' and (resid 553 through 656 )
7X-RAY DIFFRACTION7chain 'A' and (resid 657 through 739 )
8X-RAY DIFFRACTION8chain 'A' and (resid 740 through 789 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 36 )
10X-RAY DIFFRACTION10chain 'B' and (resid 37 through 108 )
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 131 )
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 162 )
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 229 )
14X-RAY DIFFRACTION14chain 'B' and (resid 230 through 253 )
15X-RAY DIFFRACTION15chain 'B' and (resid 254 through 324 )
16X-RAY DIFFRACTION16chain 'B' and (resid 325 through 346 )
17X-RAY DIFFRACTION17chain 'B' and (resid 347 through 370 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 20 )
19X-RAY DIFFRACTION19chain 'C' and (resid 21 through 30 )
20X-RAY DIFFRACTION20chain 'C' and (resid 31 through 47 )
21X-RAY DIFFRACTION21chain 'C' and (resid 48 through 74 )
22X-RAY DIFFRACTION22chain 'C' and (resid 75 through 92 )
23X-RAY DIFFRACTION23chain 'C' and (resid 93 through 107 )
24X-RAY DIFFRACTION24chain 'C' and (resid 108 through 156 )
25X-RAY DIFFRACTION25chain 'C' and (resid 157 through 174 )
26X-RAY DIFFRACTION26chain 'D' and (resid 31 through 337 )
27X-RAY DIFFRACTION27chain 'D' and (resid 338 through 417 )
28X-RAY DIFFRACTION28chain 'D' and (resid 418 through 739 )
29X-RAY DIFFRACTION29chain 'D' and (resid 740 through 790 )
30X-RAY DIFFRACTION30chain 'E' and (resid 1 through 36 )
31X-RAY DIFFRACTION31chain 'E' and (resid 37 through 131 )
32X-RAY DIFFRACTION32chain 'E' and (resid 132 through 162 )
33X-RAY DIFFRACTION33chain 'E' and (resid 163 through 266 )
34X-RAY DIFFRACTION34chain 'E' and (resid 267 through 349 )
35X-RAY DIFFRACTION35chain 'E' and (resid 350 through 370 )
36X-RAY DIFFRACTION36chain 'F' and (resid 1 through 20 )
37X-RAY DIFFRACTION37chain 'F' and (resid 21 through 30 )
38X-RAY DIFFRACTION38chain 'F' and (resid 31 through 47 )
39X-RAY DIFFRACTION39chain 'F' and (resid 48 through 57 )
40X-RAY DIFFRACTION40chain 'F' and (resid 58 through 92 )
41X-RAY DIFFRACTION41chain 'F' and (resid 93 through 156 )
42X-RAY DIFFRACTION42chain 'F' and (resid 157 through 174 )

+
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