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- PDB-7b2h: Crystal structure of the methyl-coenzyme M reductase from Methano... -

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Basic information

Entry
Database: PDB / ID: 7b2h
TitleCrystal structure of the methyl-coenzyme M reductase from Methanothermobacter Marburgensis derivatized with xenon
Components(Methyl-coenzyme M reductase I subunit ...Coenzyme-B sulfoethylthiotransferase) x 3
KeywordsTRANSFERASE / Ethyl-CoM reductase / Methyl-CoM reductase / xenon-derivatization / F430-cofactor / post-translational modification / coenzyme M / coenzyme B / thermophile / archaea.
Function / homology
Function and homology information


coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding / cytoplasm
Similarity search - Function
Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain ...Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain / Methyl-coenzyme M reductase, alpha subunit, N-terminal / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, ferredoxin-like fold / Methyl-coenzyme M reductase, alpha subunit, C-terminal / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2 / Methyl-coenzyme M reductase alpha subunit, C-terminal domain / Methyl-coenzyme M reductase alpha subunit, N-terminal domain
Similarity search - Domain/homology
1-THIOETHANESULFONIC ACID / FACTOR 430 / : / DI(HYDROXYETHYL)ETHER / Coenzyme B / XENON / Methyl-coenzyme M reductase I subunit alpha / Methyl-coenzyme M reductase I subunit beta / Methyl-coenzyme M reductase I subunit gamma
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 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 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-coenzyme M reductase I subunit alpha
B: Methyl-coenzyme M reductase I subunit beta
C: Methyl-coenzyme M reductase I subunit gamma
D: Methyl-coenzyme M reductase I subunit alpha
E: Methyl-coenzyme M reductase I subunit beta
F: Methyl-coenzyme M reductase I subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,58657
Polymers273,4296
Non-polymers6,15751
Water13,908772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60350 Å2
ΔGint-353 kcal/mol
Surface area57630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.719, 116.386, 123.070
Angle α, β, γ (deg.)90.000, 92.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Methyl-coenzyme M reductase I subunit ... , 3 types, 6 molecules ADBECF

#1: Protein Methyl-coenzyme M reductase I subunit alpha / Coenzyme-B sulfoethylthiotransferase / MCR I alpha / Coenzyme-B sulfoethylthiotransferase alpha


Mass: 60637.648 Da / Num. of mol.: 2 / Mutation: wild-type / Source method: isolated from a natural source
Details: The alpha subunit contains six modified amino acids near the active site region. Methylated His-257, Arg-271, Gln-400 and Cys-452. A thioglycine at position 445, forming a thiopeptide bond. ...Details: The alpha subunit contains six modified amino acids near the active site region. Methylated His-257, Arg-271, Gln-400 and Cys-452. A thioglycine at position 445, forming a thiopeptide bond. A didehydroaspartate residue at position 450. A methylated Arg-271
Source: (natural) Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: /
Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg
Tissue: /
References: UniProt: P11558, coenzyme-B sulfoethylthiotransferase
#2: Protein Methyl-coenzyme M reductase I subunit beta / Coenzyme-B sulfoethylthiotransferase / MCR I beta / Coenzyme-B sulfoethylthiotransferase beta


Mass: 47279.676 Da / Num. of mol.: 2 / Mutation: wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: /
Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg
Tissue: /
References: UniProt: P11560, coenzyme-B sulfoethylthiotransferase
#3: Protein Methyl-coenzyme M reductase I subunit gamma / Coenzyme-B sulfoethylthiotransferase / MCR I gamma / Coenzyme-B sulfoethylthiotransferase gamma


Mass: 28797.234 Da / Num. of mol.: 2 / Mutation: wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: /
Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg
Tissue: /
References: UniProt: P11562, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 12 types, 823 molecules

#4: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#5: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE / Coenzyme B


Mass: 343.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO7PS
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-F43 / FACTOR 430 / Cofactor F430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#11: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#12: Chemical
ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#14: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#15: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.14 Å3/Da / Density % sol: 42.52 % / Description: Butterfly intense yellow color
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7.5
Details: Crystal was obtained under aerobic condition using a crystallisation reservoir containing 27.5 % (v/v) polyethylene glycol 400, 100 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid ...Details: Crystal was obtained under aerobic condition using a crystallisation reservoir containing 27.5 % (v/v) polyethylene glycol 400, 100 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) pH 7.5, 250 mM MgCl2, 200 mM NaCl and 20 mM 2-oxoglutarate. The protein sample was in 25 mM Tris-HCl pH 7.6, 10% glycerol and 2 mM DTT at a protein concentration of 25 mg ml-1.
PH range: 7 - 8 / Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.07 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07 Å / Relative weight: 1
ReflectionResolution: 2.12→48.17 Å / Num. obs: 116190 / % possible obs: 89.36 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0902 / Rpim(I) all: 0.03796 / Rrim(I) all: 0.09807 / Net I/σ(I): 14.24
Reflection shellResolution: 2.12→2.198 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.173 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 7094 / CC1/2: 0.511 / Rpim(I) all: 0.6248 / Rrim(I) all: 1.339 / % possible all: 54.62

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A0Y

5a0y


Resolution: 2.12→48.17 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 23.02 / Stereochemistry target values: ML
Details: Riding hydrogens were added for the last refinement cycles but omitted in the deposited model
RfactorNum. reflection% reflection
Rfree0.2042 11331 5.01 %
Rwork0.1772 214664 -
obs0.1786 116155 88.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.21 Å2 / Biso mean: 50.839 Å2 / Biso min: 22.16 Å2
Refinement stepCycle: final / Resolution: 2.12→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18937 0 282 775 19994
Biso mean--51.79 51.89 -
Num. residues----2465
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 (%)
2.12-2.150.31891730.34513238341140
2.15-2.170.36062240.32474204442852
2.17-2.20.31022710.31545112538362
2.2-2.230.30333340.28716376671079
2.23-2.250.32023460.29986479682580
2.25-2.290.28653640.29066826719084
2.29-2.320.31753730.26447064743787
2.32-2.350.28453760.25317120749688
2.35-2.390.25453870.24327291767889
2.39-2.430.26373740.24027205757990
2.43-2.470.23623950.22417517791291
2.47-2.520.2523900.20667384777492
2.52-2.560.2283980.20327518791692
2.56-2.620.22633980.19897472787093
2.62-2.670.233970.20277545794293
2.67-2.740.21064040.18777650805493
2.74-2.80.20154000.18377565796594
2.8-2.880.2083960.18657593798994
2.88-2.960.21174090.17117739814895
2.96-3.060.18324050.17497674807995
3.06-3.170.20464070.17567734814195
3.17-3.30.17554060.16767725813195
3.3-3.450.2054080.16447747815595
3.45-3.630.19614100.14977726813695
3.63-3.850.15914090.14197819822896
3.85-4.150.17484090.13487733814296
4.15-4.570.14794110.13577848825996
4.57-5.230.16674080.14627867827597
5.23-6.590.20154250.1767928835398
6.59-48.170.24034240.19647965838998
Refinement TLS params.Method: refined / Origin x: 21.9668 Å / Origin y: 39.188 Å / Origin z: -32.4923 Å
111213212223313233
T0.2249 Å2-0.0038 Å2-0.0125 Å2-0.1956 Å2-0.006 Å2--0.2511 Å2
L0.4943 °20.1718 °2-0.0936 °2-0.3911 °2-0.1235 °2--0.7083 °2
S0.0005 Å °-0.0507 Å °0.0304 Å °-0.0506 Å °0.031 Å °0.05 Å °0.032 Å °-0.0542 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 550
2X-RAY DIFFRACTION1allA554 - 901
3X-RAY DIFFRACTION1allB2 - 501
4X-RAY DIFFRACTION1allC2 - 249
5X-RAY DIFFRACTION1allD3 - 549
6X-RAY DIFFRACTION1allD552 - 801
7X-RAY DIFFRACTION1allE3 - 501
8X-RAY DIFFRACTION1allF2 - 250
9X-RAY DIFFRACTION1allF301 - 401
10X-RAY DIFFRACTION1allS1 - 963
11X-RAY DIFFRACTION1allG1 - 16
12X-RAY DIFFRACTION1allH1 - 14
13X-RAY DIFFRACTION1allI2 - 3
14X-RAY DIFFRACTION1allJ1
15X-RAY DIFFRACTION1allK1 - 3

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