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- PDB-7b2c: Crystal structure of the ethyl-coenzyme M reductase from Candidat... -

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Basic information

Entry
Database: PDB / ID: 7b2c
TitleCrystal structure of the ethyl-coenzyme M reductase from Candidatus Ethanoperedens thermophilum gassed with xenon
Components(Ethyl-Coenzyme M reductase ...) x 3
KeywordsTRANSFERASE / Ethyl-CoM reductase / Methyl-CoM reductase / xenon-derivatization / 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-UWT / XENON
Function and homology information
Biological speciesCandidatus Ethanoperedens thermophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 26, 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)300,57765
Polymers293,5956
Non-polymers6,98159
Water42,2632346
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.791, 147.186, 113.376
Angle α, β, γ (deg.)90.000, 107.200, 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 / Mutation: wild-type / Source method: isolated from a natural source
Details: Seven post-translational modifications exist in the 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: Culture enrichment / Variant: / / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#2: Protein Ethyl-Coenzyme M reductase beta subunit


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


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

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Non-polymers , 12 types, 2405 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: 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
#8: 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
#9: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: K
#10: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#12: Chemical ChemComp-UWT / (2R)-2-[(2S)-2-[(2S)-2-oxidanylpropoxy]propoxy]propan-1-ol / (2~{R})-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
#13: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#14: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2346 / 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: 2.28 Å3/Da / Density % sol: 46.06 % / Description: Yellow brick of 200 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. Crystal was harvested using a MiTeGen MicroRT loop. In order to protect the crystal during xenon pressurisation, a part of the plastic capillary, usually used for room temperature diffraction experiments, was placed around it. The loop was then mounted in an Oxford Xcell xenon chamber. Xenon pressure was gradually increased using a manual pump to reach 25 bars. After 7 min, pressure was slowly released and the crystal immediately plunged in liquid nitrogen.
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: 1.54981 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54981 Å / Relative weight: 1
ReflectionResolution: 1.8→60.87 Å / Num. obs: 232772 / % possible obs: 98.1 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.046 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2 / Num. unique obs: 11640 / CC1/2: 0.739 / Rpim(I) all: 0.331 / % possible all: 94.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B1S

7b1s


Resolution: 1.8→35.9 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.116
Details: LAST REFINEMENT CYCLES WERE PERFORMED WITH HYDROGENS. HYDROGENS WERE OMITTED IN THE FINAL DEPOSITED MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 11690 5.02 %RANDOM
Rwork0.174 ---
obs0.176 232696 96.2 %-
Displacement parametersBiso max: 91.96 Å2 / Biso mean: 17.66 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-6.5101 Å20 Å2-3.9016 Å2
2---4.8187 Å20 Å2
3----1.6913 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.8→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20523 0 296 2346 23165
Biso mean--19.49 24.32 -
Num. residues----2646
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d12439SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes6797HARMONIC20
X-RAY DIFFRACTIONt_it21381HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2729SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact38301SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d41351HARMONIC50.008
X-RAY DIFFRACTIONt_angle_deg74433HARMONIC50.99
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion15.55
LS refinement shellResolution: 1.8→1.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2452 212 4.56 %
Rwork0.2093 4442 -
all0.2109 4654 -
obs--69.9 %
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)
10.077-0.04660.01770.17880.04540.12520.0005-0.04960.00390.0120.00550.0353-0.0058-0.058-0.0060.06610.0045-0.0594-0.0843-0.0174-0.0378-19.67874.369443.4465
20.12810.01570.00710.11070.08290.0785-0.0057-0.017-0.010.0321-0.0083-0.0559-0.01660.05630.0140.07530.0074-0.0895-0.0797-0.0015-0.027520.51810.223438.5745
30.2774-0.03510.08240.1371-0.03470.31040.0205-0.12480.01090.0814-0.0318-0.0316-0.02070.04170.01130.11860.0168-0.0986-0.0548-0.0261-0.12046.656110.66372.1522
40.0676-0.0026-0.07170.1690.01370.26990.0341-0.1094-0.08070.00010.0121-0.00940.0502-0.0349-0.04620.08660.0187-0.0931-0.2028-0.0053-0.0348-1.7489-22.497826.9452
5-0.03350.01230.04770.08220.0870.3124-0.01780.12190.0362-0.0472-0.00280.0259-0.02610.01990.02060.09630.0046-0.0763-0.16590.0117-0.02853.241414.870210.8924
60.13940.01780.15470.2932-0.09130.4115-0.02540.14260.0307-0.08710.03930.03420.0235-0.0332-0.01390.1250.0144-0.105-0.1408-0.0533-0.0943-10.3201-11.4968-9.8666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|595 A|1201 - A|1202 F|1101 - F|1101 }A5 - 595
2X-RAY DIFFRACTION1{ A|5 - A|595 A|1201 - A|1202 F|1101 - F|1101 }A1201 - 1202
3X-RAY DIFFRACTION1{ A|5 - A|595 A|1201 - A|1202 F|1101 - F|1101 }F1101
4X-RAY DIFFRACTION2{ B|2 - B|467 B|501 - B|501 }B2 - 467
5X-RAY DIFFRACTION2{ B|2 - B|467 B|501 - B|501 }B501
6X-RAY DIFFRACTION3{ C|2 - C|266 C|301 - C|301 }C2 - 266
7X-RAY DIFFRACTION3{ C|2 - C|266 C|301 - C|301 }C301
8X-RAY DIFFRACTION4{ D|3 - D|595 D|701 - D|703 }D3 - 595
9X-RAY DIFFRACTION4{ D|3 - D|595 D|701 - D|703 }D701 - 703
10X-RAY DIFFRACTION5{ E|2 - E|467 E|501 - E|501 }E2 - 467
11X-RAY DIFFRACTION5{ E|2 - E|467 E|501 - E|501 }E501
12X-RAY DIFFRACTION6{ B|502 - B|502 F|2 - F|266 F|1102 - F|1103 }B502
13X-RAY DIFFRACTION6{ B|502 - B|502 F|2 - F|266 F|1102 - F|1103 }F2 - 266
14X-RAY DIFFRACTION6{ B|502 - B|502 F|2 - F|266 F|1102 - F|1103 }F1102 - 1103

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