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- PDB-8rja: Crystal structure of the F420-reducing formylmethanofuran dehydro... -

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Basic information

Entry
Database: PDB / ID: 8rja
TitleCrystal structure of the F420-reducing formylmethanofuran dehydrogenase complex from the ethanotroph Candidatus Ethanoperedens thermophilum
Components
  • (Formylmethanofuran dehydrogenase subunit ...) x 3
  • Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
  • NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
  • formylmethanofuran dehydrogenase
KeywordsOXIDOREDUCTASE / Anaerobic oxidoreductase / Formylmethanofuran dehydrogenase / F420 reductase / Anaerobic ethane oxidation / formate dehydrogenase / tungstopterin / CO2 / gas channel / metalloprotein.
Function / homology
Function and homology information


NADH dehydrogenase (quinone) / allantoinase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / allantoinase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / methanogenesis, from carbon dioxide / methanogenesis / molybdopterin cofactor binding / transition metal ion binding ...NADH dehydrogenase (quinone) / allantoinase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / allantoinase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / methanogenesis, from carbon dioxide / methanogenesis / molybdopterin cofactor binding / transition metal ion binding / iron-sulfur cluster binding / oxidoreductase activity
Similarity search - Function
Formylmethanofuran dehydrogenase, subunit D / Formylmethanofuran dehydrogenase, subunit B / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus ...Formylmethanofuran dehydrogenase, subunit D / Formylmethanofuran dehydrogenase, subunit B / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Amidohydrolase 3 / Amidohydrolase family / : / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Metal-dependent hydrolase, composite domain superfamily / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Metal-dependent hydrolase / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Chem-MGD / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / : / Formylmethanofuran dehydrogenase subunit A / formylmethanofuran dehydrogenase / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic ...ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Chem-MGD / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / : / Formylmethanofuran dehydrogenase subunit A / formylmethanofuran dehydrogenase / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Formylmethanofuran dehydrogenase subunit B / Formylmethanofuran dehydrogenase subunit D
Similarity search - Component
Biological speciesCandidatus Methanoperedenaceae archaeon GB50 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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: Nat Commun / Year: 2024
Title: Ethane-oxidising archaea couple CO 2 generation to F 420 reduction.
Authors: Lemaire, O.N. / Wegener, G. / Wagner, T.
History
DepositionDec 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formylmethanofuran dehydrogenase subunit A
B: Formylmethanofuran dehydrogenase subunit B
C: formylmethanofuran dehydrogenase
D: Formylmethanofuran dehydrogenase subunit D
E: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
F: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
G: Formylmethanofuran dehydrogenase subunit A
H: Formylmethanofuran dehydrogenase subunit B
I: formylmethanofuran dehydrogenase
J: Formylmethanofuran dehydrogenase subunit D
K: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
L: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,53679
Polymers399,49512
Non-polymers13,04167
Water41,1102282
1
A: Formylmethanofuran dehydrogenase subunit A
B: Formylmethanofuran dehydrogenase subunit B
C: formylmethanofuran dehydrogenase
J: Formylmethanofuran dehydrogenase subunit D
K: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
L: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,18137
Polymers199,7486
Non-polymers6,43331
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29430 Å2
ΔGint-325 kcal/mol
Surface area58890 Å2
MethodPISA
2
D: Formylmethanofuran dehydrogenase subunit D
E: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
F: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
G: Formylmethanofuran dehydrogenase subunit A
H: Formylmethanofuran dehydrogenase subunit B
I: formylmethanofuran dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,35542
Polymers199,7486
Non-polymers6,60836
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30430 Å2
ΔGint-325 kcal/mol
Surface area58100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.627, 135.636, 149.902
Angle α, β, γ (deg.)90.00, 90.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Formylmethanofuran dehydrogenase subunit ... , 3 types, 6 molecules AGBHDJ

#1: Protein Formylmethanofuran dehydrogenase subunit A


Mass: 62582.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The lysine at position 180 is modified into carboxylysine, as in other homologs.
Source: (natural) Candidatus Methanoperedenaceae archaeon GB50 (archaea)
References: UniProt: A0A7R9MYH2, allantoinase
#2: Protein Formylmethanofuran dehydrogenase subunit B


Mass: 47081.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Methanoperedenaceae archaeon GB50 (archaea)
References: UniProt: A0A7R9R4U5
#4: Protein Formylmethanofuran dehydrogenase subunit D


Mass: 13536.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Methanoperedenaceae archaeon GB50 (archaea)
References: UniProt: A0A7R9R4V6, formylmethanofuran dehydrogenase

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Protein , 3 types, 6 molecules CIEKFL

#3: Protein formylmethanofuran dehydrogenase


Mass: 27015.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Methanoperedenaceae archaeon GB50 (archaea)
References: UniProt: A0A7R9MYM1, formylmethanofuran dehydrogenase
#5: Protein Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus


Mass: 40467.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The 8 last residues cannot be reliably modeled in the density.
Source: (natural) Candidatus Methanoperedenaceae archaeon GB50 (archaea)
References: UniProt: A0A7R9N9K9
#6: Protein NAD(P)H-quinone oxidoreductase subunit I, chloroplastic


Mass: 9065.233 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Methanoperedenaceae archaeon GB50 (archaea)
References: UniProt: A0A7R9MZV2, NADH dehydrogenase (quinone)

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Non-polymers , 15 types, 2349 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#11: 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.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#12: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#13: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#14: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: W / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#18: 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
#19: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#20: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2282 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.67 % / Description: Brown brick
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals were obtained by initial screening at 20 degrees Celsius using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization ...Details: Crystals were obtained by initial screening at 20 degrees Celsius using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 ul of mother liquor, the crystallization drop contained a mixture of 0.6 ul protein at 4.64 mg.ml-1 and 0.6 ul precipitant. The protein was in 25 mM Tris/HCl buffer pH 7.6, 10 % (v/v) glycerol, 2 mM DTT, 1 mM FAD and 1 mM FMN. The crystal was obtained in a Coy tent under an N2/H2 atmosphere (96:4 %). The crystallization reservoir contained 200 mM sodium acetate trihydrate, 100 mM sodium cacodylate, pH 6.5, and 18 % (w/v) polyethylene glycol 8,000. The crystal was soaked in the crystallization solution supplemented with 30 % (v/v) glycerol before freezing in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→57.38 Å / Num. obs: 167948 / % possible obs: 93 % / Redundancy: 7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.101 / Rrim(I) all: 0.271 / Net I/σ(I): 7.2
Reflection shellResolution: 1.973→2.187 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8397 / CC1/2: 0.621 / Rpim(I) all: 0.486 / Rrim(I) all: 1.296 / % possible all: 64.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→57.38 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.73 / Stereochemistry target values: ML
Details: The last refinement steps were performed by refining with a translation libration screw (TLS) with hydrogens modelled in the riding position. Hydrogens were omitted in the final deposited model.
RfactorNum. reflection% reflection
Rfree0.21 8349 4.97 %
Rwork0.1757 --
obs0.1774 167913 55.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.29 Å2
Refinement stepCycle: LAST / Resolution: 1.97→57.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27648 0 581 2282 30511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.339
X-RAY DIFFRACTIONf_dihedral_angle_d14.7810797
X-RAY DIFFRACTIONf_chiral_restr0.0874358
X-RAY DIFFRACTIONf_plane_restr0.0054996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-20.626810.233656X-RAY DIFFRACTION1
2-2.020.3203160.2601263X-RAY DIFFRACTION3
2.02-2.040.3403280.2466503X-RAY DIFFRACTION5
2.04-2.070.2769390.2347700X-RAY DIFFRACTION7
2.07-2.10.2692590.24311115X-RAY DIFFRACTION12
2.1-2.130.2627810.24651502X-RAY DIFFRACTION16
2.13-2.160.3082970.2361777X-RAY DIFFRACTION19
2.16-2.190.21891190.23412125X-RAY DIFFRACTION22
2.19-2.220.27891290.23732488X-RAY DIFFRACTION26
2.22-2.260.29151370.23732861X-RAY DIFFRACTION30
2.26-2.30.24741530.23613346X-RAY DIFFRACTION35
2.3-2.340.26141990.24353835X-RAY DIFFRACTION40
2.34-2.380.25572360.22914142X-RAY DIFFRACTION44
2.38-2.430.25722210.2234629X-RAY DIFFRACTION48
2.43-2.490.27162810.2284984X-RAY DIFFRACTION53
2.49-2.540.27163050.22965488X-RAY DIFFRACTION58
2.54-2.610.25673240.21745891X-RAY DIFFRACTION62
2.61-2.680.25673720.21746309X-RAY DIFFRACTION67
2.68-2.760.23273240.21316942X-RAY DIFFRACTION72
2.76-2.850.27184060.20417284X-RAY DIFFRACTION77
2.85-2.950.23863740.19577927X-RAY DIFFRACTION83
2.95-3.060.23974680.19078719X-RAY DIFFRACTION91
3.07-3.20.22274940.1889435X-RAY DIFFRACTION99
3.2-3.370.22524620.1689578X-RAY DIFFRACTION100
3.37-3.580.1975190.15189527X-RAY DIFFRACTION100
3.58-3.860.18244490.14149616X-RAY DIFFRACTION100
3.86-4.250.16975160.12619568X-RAY DIFFRACTION100
4.25-4.860.13775460.11799553X-RAY DIFFRACTION100
4.86-6.130.16964900.1549642X-RAY DIFFRACTION100
6.13-57.380.20235040.19559759X-RAY DIFFRACTION100
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)
10.43810.11120.14080.54460.08450.5253-0.0493-0.081-0.0062-0.01670.0163-0.10150.01380.12860.01010.05230.03190.00250.11550.01250.135677.074711.787934.6896
20.61910.0225-0.0630.49490.15480.48930.1084-0.21460.17130.1715-0.12340.12620.0258-0.01030.0060.1198-0.03680.05720.1886-0.06310.145161.710210.368359.5093
30.6630.1648-0.13390.42880.05970.4524-0.0018-0.10.16920.0506-0.03930.0356-0.08410.02460.02010.04180.0003-0.00480.0892-0.02850.198468.161424.914642.5836
41.19660.651-0.52071.3806-0.58640.9886-0.0119-0.2912-0.12020.1756-0.1009-0.13540.14060.17050.10920.11510.0317-0.00190.1530.00440.152471.7762-3.475350.7402
53.5706-1.55390.88082.2976-0.06141.6012-0.0934-0.1423-0.38080.124-0.05480.03350.31240.13860.150.13580.01940.06440.13130.02720.204559.8968-25.320644.0366
61.32790.1179-0.99820.9852-0.18411.4953-0.13240.1765-0.4023-0.1559-0.0254-0.06370.2983-0.04020.14460.17610.02590.00650.1331-0.03930.211964.366-26.311818.8425
70.56590.03660.01240.30270.07950.3395-0.0155-0.0777-0.06890.0196-0.07730.18670.0741-0.04010.05950.0624-0.00120.02720.0701-0.03610.177745.0067-7.642236.8656
82.61530.01271.6360.07550.0231.0257-0.0568-0.10240.08010.0745-0.04330.27380.018-0.30140.09490.1312-0.01160.07820.21-0.10830.442824.41023.292440.375
90.55720.0082-0.08740.52380.07040.3892-0.00480.0286-0.0411-0.124-0.05520.11710.05770.00070.06540.0590.01160.010.0666-0.01860.149451.9402-8.073825.2472
100.5841-0.194-0.7350.20750.34811.75220.0261-0.0429-0.0045-0.067-0.0365-0.13220.08980.27660.01830.12110.04370.01430.14020.00890.166269.1211-14.678128.7706
111.1844-0.02090.68180.3031-0.85862.7650.10750.39310.1405-0.61650.01230.14250.113-0.0974-0.07880.43090.045-0.07420.33920.10520.228255.82847.7093-3.5863
121.2874-0.90860.65982.3005-1.33821.03370.16050.62260.4368-0.6867-0.2964-0.1658-0.22280.17130.0960.47360.02060.02750.3130.09910.272261.734511.7878-4.5368
130.6640.2813-0.77952.4659-1.67391.6861-0.00590.4380.2835-0.4595-0.02860.2171-0.0506-0.0741-0.05920.38460.021-0.11480.21520.05390.25351.137111.8114-2.5214
141.6218-0.04930.15690.1376-0.59472.57540.07650.29880.0699-0.4182-0.02150.1424-0.12840.2074-0.04750.32660.0546-0.08530.18630.03540.188548.909514.10653.1893
151.6839-0.12770.12430.8345-0.24721.68220.06940.33280.155-0.2835-0.04570.1718-0.14740.0257-0.06160.23980.0358-0.11540.13120.02960.248943.568510.82188.6834
160.5918-0.16120.0380.27820.01880.0688-0.01510.06560.1101-0.1366-0.03290.1464-0.0549-0.03230.09340.16610.0851-0.16280.16580.01790.324335.201812.831115.9226
171.6941-0.27520.72710.3248-0.58341.17050.04860.081-0.0152-0.1307-0.08240.19990.0122-0.14580.00650.17450.0366-0.14780.2208-0.08290.476323.575111.806522.5971
182.4588-0.84450.0160.3331-0.24811.35050.14610.35460.384-0.2538-0.12520.1479-0.1267-0.1678-0.00230.32510.1515-0.20510.3351-0.08050.608818.796819.5518.3883
193.11890.33841.82240.59170.00883.3717-0.12290.09150.2027-0.2487-0.07130.3462-0.0815-0.17270.10260.14010.0143-0.11850.1811-0.05560.410526.266316.656324.7411
201.26690.17720.74272.5002-0.33347.14750.0941-0.0643-0.15870.3386-0.0129-0.08420.0672-0.0777-0.08090.28090.08070.00980.1829-0.06980.32183.89666.352958.2638
210.15660.26250.12030.87260.01230.177-0.03960.0003-0.0066-0.01640.0213-0.0571-0.1424-0.0471-0.09320.2680.06370.05190.1302-0.08920.33814.877779.227839.4787
224.306-2.94840.76745.27440.26067.3014-0.1668-0.16630.45080.17380.0624-0.0725-0.4761-0.04630.10240.34940.03730.07630.147-0.10020.35857.250183.194345.6078
232.31.67362.27335.5665-1.63064.73010.0758-0.390.26550.52210.09910.3615-0.2133-0.7389-0.18920.32850.12230.10050.303-0.0220.3978-1.511374.203760.3206
240.91941.06680.25361.3912-0.0120.6837-0.0004-0.14860.14290.10980.0287-0.0203-0.1527-0.1698-0.00910.27040.06840.01220.1429-0.07530.22735.076873.011755.4609
250.6734-0.1578-0.5821.91490.80192.0444-0.047-0.05890.13690.30560.1591-0.1619-0.14920.3134-0.09160.13080.0327-0.04410.1441-0.06250.186810.970466.864352.3249
260.9866-1.18940.80493.6231-0.39291.0003-0.1416-0.00650.193-0.00350.0282-0.2424-0.2880.21330.05550.365-0.0546-0.11210.2923-0.1310.522521.316977.052246.5561
271.37410.6259-0.54451.1384-0.22960.95510.02330.23680.0439-0.0805-0.02610.0699-0.0208-0.21240.07650.20650.17690.05110.30490.00440.234-41.657975.578243.3771
282.1435-0.152-0.97681.00840.16812.70210.13480.2040.095-0.2827-0.07450.0964-0.0061-0.2336-0.06270.17090.12180.01020.206-0.01860.2464-34.647976.083537.5882
291.124-0.5121-0.59120.67080.44690.8895-0.173-0.41150.17670.36020.2187-0.14050.06850.1698-0.05750.34240.1720.0340.2943-0.01050.2608-35.707983.264768.1683
302.3758-1.1188-0.72990.7070.14942.07310.08880.20210.4524-0.0313-0.04630.0668-0.437-0.2985-0.06190.26760.1410.05690.27610.03240.2387-48.618487.075361.8926
311.059-0.4602-0.52181.8566-0.04331.32960.0904-0.07210.3037-0.0874-0.0761-0.0891-0.14650.058-0.03230.20180.10740.00540.2238-0.01450.2301-32.240284.707554.2257
321.07750.0507-0.59581.57890.1521.5781-0.1565-0.0954-0.03210.27360.09920.01260.0817-0.11410.06440.3150.1630.02470.30810.01980.177-46.993475.489169.5245
332.4951-0.13360.13113.06132.22771.9787-0.0229-0.1333-0.53230.29530.12010.03961.15580.0481-0.09410.57940.08070.07290.27780.08640.4564-40.78860.445567.5385
340.5698-1.10830.09383.8962-1.47880.9807-0.0304-0.05480.6798-0.245-0.12750.2687-0.4531-0.41160.16490.42150.20780.0820.3094-0.05060.5481-25.40794.917138.6989
350.67770.04720.52660.0464-0.10510.8786-0.0741-0.06450.27560.040.0669-0.1501-0.1302-0.02670.02310.21220.13260.06730.12730.01130.2439-14.643881.117135.0894
361.19050.2951.21770.23620.27961.62550.18150.1107-0.2139-0.0603-0.0002-0.10920.1270.0769-0.11680.2090.14160.0390.24660.09370.2682-25.790879.075723.7991
373.9495-0.55940.55323.45511.68721.00090.28470.54910.2711-0.5123-0.1084-0.0724-0.2284-0.0405-0.09380.32150.16080.07620.26090.06390.2084-19.76883.681918.5709
381.4128-0.3409-0.40890.09040.11090.13530.02140.03430.26070.01160.0388-0.078-0.1159-0.07430.00890.31680.12080.08930.15670.03040.3414-19.422587.971931.2263
390.79270.8157-0.12732.06570.40291.8716-0.0936-0.24390.43430.08830.09320.0664-0.3256-0.15860.08660.25470.15970.05490.20570.0030.352-21.105385.099641.3911
402.5362-0.3996-0.43531.0645-0.21251.1987-0.05640.3114-0.0847-0.32380.0429-0.29520.07310.02140.0050.1758-0.02020.07090.1374-0.04290.200916.077942.9158-15.88
410.15110.20360.12590.43130.17151.209-0.03470.01620.0538-0.05120.0299-0.0674-0.02090.02450.0090.0556-0.01330.04620.0299-0.01650.18710.54646.280912.8231
420.7016-0.2828-0.10060.20350.2330.42150.0257-0.02270.0978-0.0720.0036-0.026-0.1088-0.0837-0.03560.11020.02240.04530.090.06230.1863-5.891255.44237.9947
430.7999-0.02190.18340.44530.30210.44010.05110.09260.0668-0.0679-0.02440.0834-0.0953-0.2927-0.01420.05830.04470.00260.17810.03230.1205-19.22452.52018.3393
440.4443-0.45780.28441.0777-0.40931.0579-0.1624-0.0079-0.2113-0.0850.0869-0.07910.129-0.2680.04810.0863-0.02810.03120.15840.02640.1603-17.326740.35794.9309
450.42550.0895-0.08531.4024-0.94361.698-0.00470.0643-0.0804-0.0611-0.00460.07860.0143-0.15040.01370.023-0.02080.0150.12530.01060.1725-14.55536.12814.6597
460.2406-0.1399-0.23380.22450.10740.7641-0.03250.0413-0.0496-0.06120.0595-0.00870.0512-0.1398-0.02540.0515-0.03350.0350.10250.0120.1678-6.794335.847311.8544
470.30860.15930.03920.538-0.14770.2197-0.05180.0007-0.20640.0110.0081-0.07290.1772-0.0599-0.03560.1186-0.05440.09410.0345-0.01170.20652.63623.39347.9695
480.57870.167-0.18320.6043-0.25670.8211-0.03950.1314-0.0479-0.12920.0904-0.09770.0727-0.0626-0.05090.1226-0.03260.07250.0861-0.03090.19347.399635.3933-4.7198
491.0876-0.6263-0.23941.01450.53860.65380.05050.13780.1625-0.1215-0.02250.0161-0.2219-0.1176-0.02550.1850.04950.03580.10320.08030.2194-6.643263.69474.4498
500.17420.0470.30470.9098-0.44920.84860.06420.10520.3307-0.187-0.0039-0.1561-0.3914-0.03920.08010.28230.06590.09980.10180.03190.322-3.655282.187922.0947
510.7555-0.0968-0.25270.5230.04230.29110.0688-0.03880.18250.00620.0592-0.2909-0.25340.1284-0.05110.2961-0.0560.0930.1311-0.05360.451221.077580.471128.1216
520.0665-0.01180.02320.2341-0.00230.21450.0143-0.0150.06680.02490.0616-0.0102-0.1794-0.0960.01630.10.1030.080.02220.0140.2116-3.035162.992931.8641
530.3552-0.80320.23313.102-0.0580.32440.0567-0.01050.14760.11710.0478-0.0018-0.1162-0.1076-0.06730.12780.06340.04670.15140.04680.147-10.372554.063447.6929
541.5-0.20721.15550.79160.2662.5519-0.1276-0.2634-0.01640.22050.16480.2732-0.0695-0.4723-0.0190.12890.04940.08030.22130.05440.2325-16.529447.516549.4301
550.1524-0.0338-0.04940.46470.05490.3866-0.02470.00010.19060.01960.078-0.0884-0.12070.0234-0.03510.08080.02410.01190.048-0.00710.23058.781961.329432.9447
560.33270.22220.15920.3675-0.09420.25810.08020.10990.2566-0.17460.0403-0.2192-0.16630.0456-0.06820.2096-0.01450.0850.11120.01410.306213.298271.319317.5558
570.75440.21720.50940.73650.10750.6033-0.22820.01220.23320.21090.1154-0.3494-0.1060.06180.01840.09870.0064-0.04390.114-0.05420.33136.046942.837136.9671
580.9847-1.50560.5072.8071-0.82260.28860.05080.00630.1393-0.2039-0.0942-0.27550.0310.16560.0340.0987-0.00030.04860.1471-0.03010.345539.024139.752931.1632
592.1983-1.2246-0.57191.5665-0.00081.1028-0.0362-0.0699-0.04340.18670.0608-0.090.04460.0526-0.00990.06260.0249-0.02310.1014-0.02110.206527.276137.239940.4529
601.952-0.0735-0.32061.10530.12481.4919-0.1305-0.1194-0.09730.16810.13040.05860.1099-0.0214-0.00870.08940.03770.01210.09630.01630.14811.538637.76846.1101
612.7935-0.12641.55052.1141-0.08712.3911-0.1086-0.4149-0.29860.38130.09370.14760.1696-0.112-0.03830.17940.08640.06560.23640.08910.233-0.909432.760455.3577
625.09991.62631.97220.97260.44432.0251-0.09390.07560.1364-0.2404-0.02080.28360.0162-0.3940.11290.18150.0142-0.10480.1788-0.07310.260628.1612-18.333620.8929
631.4009-1.6049-0.27982.28161.3842.6078-0.056-0.1041-0.07070.0485-0.0851-0.27890.2909-0.00170.12850.1249-0.02660.03750.1002-0.02670.33847.5782-26.575729.2622
643.5494-2.47560.62822.64870.61965.29330.01990.1119-0.6934-0.2571-0.00040.18110.7841-0.4447-0.00670.2234-0.0804-0.00950.1438-0.04780.29343.5534-31.922925.526
650.60660.84190.87725.31410.81385.4264-0.0915-0.2701-0.14360.1973-0.13470.72170.0179-0.50340.20610.2498-0.05770.06830.2397-0.02220.401425.4389-26.083226.1178
662.67711.0497-0.9873.3294-1.01622.00540.1098-0.1731-0.2362-0.0047-0.05540.3107-0.0198-0.3012-0.01770.172-0.0358-0.05010.1834-0.02470.300829.7966-26.431517.8962
671.35810.59520.01091.8658-0.38370.72510.05120.0761-0.1445-0.1467-0.12590.05770.1252-0.12490.04860.1082-0.0154-0.01390.1372-0.06350.21135.0748-20.343620.2888
684.7516-1.23341.92217.0535-1.94035.8633-0.18410.4005-0.1774-0.7772-0.0536-0.28160.19130.08410.22050.3691-0.03670.07220.2501-0.12490.422347.9038-26.654110.1819
693.32390.6035-0.83530.1479-0.33671.11660.2051-0.14880.39170.1092-0.04970.0593-0.24060.1229-0.18180.3779-0.11230.26570.2789-0.09050.458222.8021-15.023767.3776
701.41830.4701-0.39060.3452-0.18640.51550.0688-0.1975-0.13070.1425-0.05950.32670.0268-0.0588-0.04510.2995-0.06820.21520.2437-0.06090.493319.1177-24.901760.8953
710.67480.30330.18840.48550.22780.22420.0912-0.1109-0.10350.11310.02160.1154-0.0059-0.08270.17580.3217-0.08190.24480.26860.0070.69625.3691-36.869164.0896
722.4521-0.0634-0.35380.5744-0.49591.00190.0724-0.1641-0.02790.2473-0.07160.191-0.0044-0.05730.02740.2847-0.06440.1720.2213-0.0220.506514.3584-29.073661.5609
731.87250.2473-0.20620.8209-0.17211.88840.1572-0.0272-0.1780.16630.10680.3268-0.1368-0.4117-0.21630.31880.01150.17710.34370.02540.773-2.9297-25.426159.5599
745.59642.12452.04584.20292.09114.9396-0.14730.10930.9986-0.0813-0.10780.2933-0.8144-0.16690.25770.57970.10670.0940.32670.04420.85490.372-9.991655.323
753.37751.34140.2652.5457-2.11922.5937-0.1739-0.6751-0.66650.4963-0.14570.31140.711-0.07640.28820.4527-0.09830.16990.35310.01060.526737.8923-36.70159.7595
764.3073-1.6859-2.0513.5777-1.4772.7809-0.08410.1348-0.09980.0443-0.26680.1990.1390.00250.26730.1176-0.05160.06080.12010.00420.12243.3073-26.219848.8515
775.8760.73354.07971.18272.08115.3947-0.10710.23270.4183-0.0296-0.1087-0.0487-0.4260.27480.12660.3489-0.02710.1460.25580.08540.281648.5673-21.314863.1804
781.8236-1.243-0.28891.96782.17123.52370.0644-0.2749-0.18840.294-0.0931-0.13020.30240.22030.00980.2266-0.03030.07540.23260.07910.322756.3579-25.221660.3777
796.02191.157-3.61182.0542-2.54058.5455-0.0858-0.0467-0.38280.1909-0.17830.01170.5480.0770.24010.22740.02150.04750.090.03360.233848.91-30.777649.7899
803.1426-1.15791.26110.6669-1.39534.5018-0.2166-0.32-0.6797-0.04650.04890.07680.47560.24860.24340.2784-0.03070.12070.24210.07310.23942.7408-32.990662.0145
811.45440.3684-0.60210.5507-0.46991.30960.0208-0.0686-0.07020.0349-0.106-0.00480.105-0.0590.09580.1649-0.04380.11180.1342-0.01870.29736.3878-24.970951.1004
823.55083.42852.22744.9541.09152.0792-0.1889-0.2774-1.08630.0740.1116-0.12210.9989-0.35080.160.35-0.05420.12210.22390.05450.427133.599-39.541355.5026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 253 )
3X-RAY DIFFRACTION3chain 'A' and (resid 254 through 502 )
4X-RAY DIFFRACTION4chain 'A' and (resid 503 through 567 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 35 )
6X-RAY DIFFRACTION6chain 'B' and (resid 36 through 77 )
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 216 )
8X-RAY DIFFRACTION8chain 'B' and (resid 217 through 244 )
9X-RAY DIFFRACTION9chain 'B' and (resid 245 through 389 )
10X-RAY DIFFRACTION10chain 'B' and (resid 390 through 430 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 22 )
12X-RAY DIFFRACTION12chain 'C' and (resid 23 through 61 )
13X-RAY DIFFRACTION13chain 'C' and (resid 62 through 79 )
14X-RAY DIFFRACTION14chain 'C' and (resid 80 through 105 )
15X-RAY DIFFRACTION15chain 'C' and (resid 106 through 143 )
16X-RAY DIFFRACTION16chain 'C' and (resid 144 through 206 )
17X-RAY DIFFRACTION17chain 'C' and (resid 207 through 225 )
18X-RAY DIFFRACTION18chain 'C' and (resid 226 through 239 )
19X-RAY DIFFRACTION19chain 'C' and (resid 240 through 253 )
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 10 )
21X-RAY DIFFRACTION21chain 'D' and (resid 11 through 24 )
22X-RAY DIFFRACTION22chain 'D' and (resid 25 through 31 )
23X-RAY DIFFRACTION23chain 'D' and (resid 32 through 44 )
24X-RAY DIFFRACTION24chain 'D' and (resid 45 through 86 )
25X-RAY DIFFRACTION25chain 'D' and (resid 87 through 116 )
26X-RAY DIFFRACTION26chain 'D' and (resid 117 through 125 )
27X-RAY DIFFRACTION27chain 'E' and (resid 1 through 43 )
28X-RAY DIFFRACTION28chain 'E' and (resid 44 through 75 )
29X-RAY DIFFRACTION29chain 'E' and (resid 76 through 132 )
30X-RAY DIFFRACTION30chain 'E' and (resid 133 through 163 )
31X-RAY DIFFRACTION31chain 'E' and (resid 164 through 217 )
32X-RAY DIFFRACTION32chain 'E' and (resid 218 through 326 )
33X-RAY DIFFRACTION33chain 'E' and (resid 327 through 351 )
34X-RAY DIFFRACTION34chain 'F' and (resid 5 through 12 )
35X-RAY DIFFRACTION35chain 'F' and (resid 13 through 26 )
36X-RAY DIFFRACTION36chain 'F' and (resid 27 through 34 )
37X-RAY DIFFRACTION37chain 'F' and (resid 35 through 46 )
38X-RAY DIFFRACTION38chain 'F' and (resid 47 through 65 )
39X-RAY DIFFRACTION39chain 'F' and (resid 66 through 81 )
40X-RAY DIFFRACTION40chain 'G' and (resid 2 through 48 )
41X-RAY DIFFRACTION41chain 'G' and (resid 49 through 109 )
42X-RAY DIFFRACTION42chain 'G' and (resid 110 through 159 )
43X-RAY DIFFRACTION43chain 'G' and (resid 160 through 223 )
44X-RAY DIFFRACTION44chain 'G' and (resid 224 through 253 )
45X-RAY DIFFRACTION45chain 'G' and (resid 254 through 286 )
46X-RAY DIFFRACTION46chain 'G' and (resid 287 through 389 )
47X-RAY DIFFRACTION47chain 'G' and (resid 390 through 419 )
48X-RAY DIFFRACTION48chain 'G' and (resid 420 through 502 )
49X-RAY DIFFRACTION49chain 'G' and (resid 503 through 567 )
50X-RAY DIFFRACTION50chain 'H' and (resid 2 through 35 )
51X-RAY DIFFRACTION51chain 'H' and (resid 36 through 77 )
52X-RAY DIFFRACTION52chain 'H' and (resid 78 through 192 )
53X-RAY DIFFRACTION53chain 'H' and (resid 193 through 216 )
54X-RAY DIFFRACTION54chain 'H' and (resid 217 through 244 )
55X-RAY DIFFRACTION55chain 'H' and (resid 245 through 389 )
56X-RAY DIFFRACTION56chain 'H' and (resid 390 through 430 )
57X-RAY DIFFRACTION57chain 'I' and (resid 1 through 22 )
58X-RAY DIFFRACTION58chain 'I' and (resid 23 through 61 )
59X-RAY DIFFRACTION59chain 'I' and (resid 62 through 124 )
60X-RAY DIFFRACTION60chain 'I' and (resid 125 through 206 )
61X-RAY DIFFRACTION61chain 'I' and (resid 207 through 253 )
62X-RAY DIFFRACTION62chain 'J' and (resid 2 through 10 )
63X-RAY DIFFRACTION63chain 'J' and (resid 11 through 24 )
64X-RAY DIFFRACTION64chain 'J' and (resid 25 through 31 )
65X-RAY DIFFRACTION65chain 'J' and (resid 32 through 44 )
66X-RAY DIFFRACTION66chain 'J' and (resid 45 through 58 )
67X-RAY DIFFRACTION67chain 'J' and (resid 59 through 116 )
68X-RAY DIFFRACTION68chain 'J' and (resid 117 through 126 )
69X-RAY DIFFRACTION69chain 'K' and (resid 1 through 22 )
70X-RAY DIFFRACTION70chain 'K' and (resid 23 through 109 )
71X-RAY DIFFRACTION71chain 'K' and (resid 110 through 163 )
72X-RAY DIFFRACTION72chain 'K' and (resid 164 through 234 )
73X-RAY DIFFRACTION73chain 'K' and (resid 235 through 326 )
74X-RAY DIFFRACTION74chain 'K' and (resid 327 through 351 )
75X-RAY DIFFRACTION75chain 'L' and (resid 5 through 12 )
76X-RAY DIFFRACTION76chain 'L' and (resid 13 through 26 )
77X-RAY DIFFRACTION77chain 'L' and (resid 27 through 34 )
78X-RAY DIFFRACTION78chain 'L' and (resid 35 through 46 )
79X-RAY DIFFRACTION79chain 'L' and (resid 47 through 56 )
80X-RAY DIFFRACTION80chain 'L' and (resid 57 through 65 )
81X-RAY DIFFRACTION81chain 'L' and (resid 66 through 75 )
82X-RAY DIFFRACTION82chain 'L' and (resid 76 through 82 )

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  • 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

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