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- PDB-7b1s: Crystal structure of the ethyl-coenzyme M reductase from Candidat... -

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Basic information

Entry
Database: PDB / ID: 7b1s
TitleCrystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum at 0.994-A resolution
Components(Ethyl-Coenzyme M reductase ...) x 3
KeywordsTRANSFERASE / Ethyl-CoM reductase / Methyl-CoM reductase / ethane-oxidizers / F430-cofactor / post-translational modification / gas channel / coenzyme M / coenzyme B / true atomic resolution / thermophile / archaea.
Function / homology1-THIOETHANESULFONIC ACID / : / : / Coenzyme B / Dimethylated-F430 cofactor / Chem-UUT
Function and homology information
Biological speciesCandidatus Ethanoperedens thermophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.992 Å
AuthorsWagner, T. / Lemaire, O.N. / Engilberge, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)EXC-2077 390741603 Germany
CitationJournal: Science / Year: 2021
Title: Crystal structure of a key enzyme for anaerobic ethane activation.
Authors: Hahn, C.J. / Lemaire, O.N. / Kahnt, J. / Engilberge, S. / Wegener, G. / Wagner, T.
History
DepositionNov 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ethyl-Coenzyme M reductase alpha subunit
B: Ethyl-Coenzyme M reductase beta subunit
C: Ethyl-Coenzyme M reductase gamma subunit
D: Ethyl-Coenzyme M reductase alpha subunit
E: Ethyl-Coenzyme M reductase beta subunit
F: Ethyl-Coenzyme M reductase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,85731
Polymers293,5956
Non-polymers4,26225
Water55,5943086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62500 Å2
ΔGint-307 kcal/mol
Surface area61010 Å2
Unit cell
Length a, b, c (Å)83.736, 146.927, 113.128
Angle α, β, γ (deg.)90.000, 106.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Ethyl-Coenzyme M reductase ... , 3 types, 6 molecules ADBECF

#1: Protein Ethyl-Coenzyme M reductase alpha subunit


Mass: 66344.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Seven post-translational modifications exist in this subunit: N1-methylhistidine291 5(S)-methylarginine305 S-methylcysteine354 3-methylisoleucine377 2(S)-methylglutamine445 Thioglycine490 N2-methylhistidine491
Source: (natural) Candidatus Ethanoperedens thermophilum (archaea)
Cell line: / / Organ: / / Plasmid details: Enrichment culture / Variant: / / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#2: Protein Ethyl-Coenzyme M reductase beta subunit


Mass: 49874.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Ethanoperedens thermophilum (archaea)
Cell line: / / Organ: / / Plasmid details: Enrichment culture / Variant: / / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#3: Protein Ethyl-Coenzyme M reductase gamma subunit


Mass: 30578.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Ethanoperedens thermophilum (archaea)
Cell line: / / Organ: / / Plasmid details: Enrichment culture / Variant: / / Tissue: / / References: coenzyme-B sulfoethylthiotransferase

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Non-polymers , 10 types, 3111 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO7PS / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Chemical ChemComp-USN / Dimethylated-F430 cofactor


Mass: 934.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H55N6NiO13 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-UUT / (2S)-2-{[(2S)-2-{[(2S)-2-hydroxypropyl]oxy}propyl]oxy}propan-1-ol / (2~{S})-2-[(2~{S})-2-[(2~{S})-2-oxidanylpropoxy]propoxy]propan-1-ol


Mass: 192.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O4
Details: Pentaerythritol propoxylate, a crystallization agent, is likely the source of the fragment modeled.
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3086 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.87 % / Description: Yellow brick of 250 um long.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystals were obtained by initial screening at 20 degree 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 degree 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, crystallization drop contained a mixture of 0.6 ul protein at 16.22 mg.ml-1 and 0.6 ul precipitant. The crystal was obtained by initial screening using the JBScreen Pentaerythritol screen from Jena Bioscience in a Coy tent under an N2/H2 atmosphere (95:5 %). The crystallization reservoir contained 45 % (w/v) Pentaerythritol Propoxylate (5/4 PO/OH), 100 mM Tris pH 8.5 and 400 mM potassium chloride.
PH range: 7.5 - 8.5 / Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 0.992→108.19 Å / Num. obs: 1061996 / % possible obs: 89.1 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.047 / Rrim(I) all: 0.125 / Net I/σ(I): 9.7
Reflection shellResolution: 0.992→1.07 Å / Rmerge(I) obs: 1.167 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 53103 / CC1/2: 0.563 / Rpim(I) all: 0.476 / Rrim(I) all: 1.262 / % possible all: 58.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A8W

5a8w


Resolution: 0.992→39.76 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.99 / Stereochemistry target values: ML
Details: Refinement was performed with hydrogens in riding positions
RfactorNum. reflection% reflection
Rfree0.1275 52845 5.05 %
Rwork0.1119 992599 -
obs0.1127 1045444 73.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.64 Å2 / Biso mean: 10.6019 Å2 / Biso min: 3.16 Å2
Refinement stepCycle: final / Resolution: 0.992→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20525 0 261 3086 23872
Biso mean--10.52 23.51 -
Num. residues----2646
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.99-1.010.2339160.22433353511
1.01-1.020.2323920.2299170117934
1.02-1.030.23342550.22864571482610
1.03-1.040.24344720.22738198867018
1.04-1.060.2366370.2178119361257326
1.06-1.070.21928320.2066160671689936
1.07-1.090.21379850.2008201572114245
1.09-1.10.21412070.1977240272523453
1.1-1.120.211914880.1949282812976963
1.12-1.140.212316640.1895328603452473
1.14-1.160.205319860.181369763896282
1.16-1.180.199720730.1733397234179688
1.18-1.20.187521430.1693405124265590
1.2-1.230.187321980.158410434324191
1.23-1.250.164522350.1395411924342791
1.25-1.280.152222000.1293413964359692
1.28-1.310.147323280.1257416424397093
1.31-1.350.142622660.1154419814424793
1.35-1.390.133521870.1116421354432293
1.39-1.430.130723090.1052423114462094
1.43-1.490.118223590.0963423354469494
1.49-1.550.110523670.0896425834495095
1.55-1.620.108522490.0871429784522795
1.62-1.70.10222440.0843430924533696
1.7-1.810.100523030.0853433504565396
1.81-1.950.098422980.0863436524595097
1.95-2.140.094422180.084439494616797
2.14-2.450.095723310.0843441424647398
2.45-3.090.10423390.0957445224686198
3.09-39.760.118525640.1103449524751699

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