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- PDB-7nkg: Methyl-coenzyme M reductase from Methermicoccus shengliensis at 1... -

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Basic information

Entry
Database: PDB / ID: 7nkg
TitleMethyl-coenzyme M reductase from Methermicoccus shengliensis at 1.6-A resolution
Components(Methyl-coenzyme M reductase ...) x 3
KeywordsTRANSFERASE / Methyl-coenzyme M reductase / cofactor F430 / post-translational modification / archaea / methoxydotrophy / methanogenesis / coenzyme M / coenzyme B / heterodisulfide / radical mechanism / thermophile / thioglycine
Function / homology1-THIOETHANESULFONIC ACID / FACTOR 430 / : / Coenzyme B
Function and homology information
Biological speciesMethermicoccus shengliensis DSM 18856 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMueller, M. / Wagner, T.
Funding support Germany, Netherlands, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
Netherlands Organisation for Scientific Research (NWO)Gravitation grant 024.002.002 Netherlands
German Research Foundation (DFG)3768/1-1 Germany
CitationJournal: Microorganisms / Year: 2021
Title: Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications.
Authors: Kurth, J.M. / Muller, M.C. / Welte, C.U. / Wagner, T.
History
DepositionFeb 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 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: Methyl-coenzyme M reductase alpha subunit
B: Methyl-coenzyme M reductase beta subunit
C: Methyl-coenzyme M reductase gamma subunit
D: Methyl-coenzyme M reductase alpha subunit
E: Methyl-coenzyme M reductase beta subunit
F: Methyl-coenzyme M reductase gamma subunit
G: Methyl-coenzyme M reductase alpha subunit
H: Methyl-coenzyme M reductase beta subunit
I: Methyl-coenzyme M reductase gamma subunit
J: Methyl-coenzyme M reductase alpha subunit
K: Methyl-coenzyme M reductase beta subunit
L: Methyl-coenzyme M reductase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)551,71634
Polymers545,31212
Non-polymers6,40322
Water77,4284298
1
A: Methyl-coenzyme M reductase alpha subunit
B: Methyl-coenzyme M reductase beta subunit
C: Methyl-coenzyme M reductase gamma subunit
D: Methyl-coenzyme M reductase alpha subunit
E: Methyl-coenzyme M reductase beta subunit
F: Methyl-coenzyme M reductase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,04419
Polymers272,6566
Non-polymers3,38813
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
G: Methyl-coenzyme M reductase alpha subunit
H: Methyl-coenzyme M reductase beta subunit
I: Methyl-coenzyme M reductase gamma subunit
J: Methyl-coenzyme M reductase alpha subunit
K: Methyl-coenzyme M reductase beta subunit
L: Methyl-coenzyme M reductase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,67215
Polymers272,6566
Non-polymers3,0159
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.615, 148.177, 235.415
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Methyl-coenzyme M reductase ... , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
Methyl-coenzyme M reductase alpha subunit


Mass: 62295.250 Da / Num. of mol.: 4 / Mutation: wild-type / Source method: isolated from a natural source
Details: The polypeptide contains three post-translational modifications: Methylhistidine-275 Methylarginine-289 Thioglycine-463
Source: (natural) Methermicoccus shengliensis DSM 18856 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ZC-1 / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#2: Protein
Methyl-coenzyme M reductase beta subunit


Mass: 45908.246 Da / Num. of mol.: 4 / Mutation: wild-type / Source method: isolated from a natural source
Source: (natural) Methermicoccus shengliensis DSM 18856 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ZC-1 / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#3: Protein
Methyl-coenzyme M reductase gamma subunit


Mass: 28124.594 Da / Num. of mol.: 4 / Mutation: wild-type / Source method: isolated from a natural source
Source: (natural) Methermicoccus shengliensis DSM 18856 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ZC-1 / Tissue: / / References: coenzyme-B sulfoethylthiotransferase

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Non-polymers , 7 types, 4320 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O3S2
#7: Chemical
ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H22NO7PS
#8: Chemical
ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4298 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.12 %
Description: Yellow thick brick-shape crystals appeared within two weeks
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The protein sample was at 47 g/l in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol and 2 mM dithiothreitol. MCR crystals were obtained aerobically by using the sitting drop method on 96-Well MRC 2- ...Details: The protein sample was at 47 g/l in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol and 2 mM dithiothreitol. MCR crystals were obtained aerobically by using the sitting drop method on 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 sample and 0.6 ul of crystallization solution. The crystallization solution contained 25% w/v polyethylene glycol 3350, 100 mM Bis-Tris pH 5.5 and 200 mM lithium sulfate.
PH range: / / Temp details: /

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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 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→49.41 Å / Num. obs: 602614 / % possible obs: 99.7 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.051 / Rrim(I) all: 0.105 / Net I/σ(I): 8.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.216 / Mean I/σ(I) obs: 1 / Num. unique obs: 87124 / CC1/2: 0.356 / Rpim(I) all: 0.661 / Rrim(I) all: 1.388 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E6Y

1e6y


Resolution: 1.6→48.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.09 / SU Rfree Blow DPI: 0.083 / SU Rfree Cruickshank DPI: 0.081
Details: The last cycle of refinement was performed with hydrogens in riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 30001 4.98 %RANDOM
Rwork0.1725 ---
obs0.1734 602442 99.7 %-
Displacement parametersBiso max: 136.35 Å2 / Biso mean: 42.85 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.7622 Å20 Å20 Å2
2---3.8335 Å20 Å2
3---2.0712 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.6→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37962 0 405 4298 42665
Biso mean--27.38 39.25 -
Num. residues----4960
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d23283SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes12500HARMONIC5
X-RAY DIFFRACTIONt_it39274HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5120SEMIHARMONIC5
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_contact68074SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d76578HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg138068HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion16.45
LS refinement shellResolution: 1.6→1.61 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2451 614 5.1 %
Rwork0.2342 11435 -
all0.2347 12049 -
obs--99.01 %
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)
10.17560.0325-0.04610.2257-0.07020.2111-0.01670.0205-0.0085-0.0244-0.0116-0.05130.00440.02660.0283-0.09290.00380.0091-0.0660.0008-0.070510.371844.5076-41.4697
20.16610.0106-0.03480.2371-0.11040.2465-0.01530.0147-0.0571-0.02270.02480.06190.0632-0.0869-0.0095-0.0843-0.02080.009-0.0589-0.0075-0.052-19.623130.323-31.0902
30.19710.0495-0.13080.2768-0.1460.33870.0215-0.04260.06090.13120.00660.0418-0.1382-0.0437-0.0281-0.02330.02130.0213-0.0571-0.0084-0.0765-9.646570.5561-18.4394
40.17410.0085-0.02620.2795-0.11910.2525-0.006-0.0907-0.00490.1385-0.0155-0.034-0.07120.03230.0215-0.04590.0001-0.0042-0.03210.0061-0.09620.572943.40780.8147
50.29870.002-0.07190.3028-0.15130.4680.01770.08920.0737-0.00470.01110.0379-0.115-0.0818-0.0288-0.03670.0392-0.0387-0.0001-0.0717-0.002-2.458379.3797-51.7699
60.18410.004-0.08480.4411-0.04490.3168-0.0332-0.1007-0.10470.07760.0212-0.00750.071-0.00630.012-0.07730.0130.0284-0.07960.0424-0.0689-5.7569.4095-1.5113
70.8830.65270.58390.71770.4041.3292-0.4111-0.13160.4874-0.39940.00120.3239-0.6323-0.41530.40990.14390.1387-0.271-0.0165-0.05190.0285-58.146856.6962-84.6817
80.83660.48680.64390.74540.48791.3260.1062-0.435-0.01560.085-0.17540.00610.0894-0.5720.0692-0.1384-0.0496-0.01780.2336-0.0015-0.0874-56.292730.9526-61.7165
90.94540.83760.75751.46850.60891.2377-0.17550.2688-0.2126-0.42940.29-0.2464-0.10010.1708-0.11450.0261-0.06660.08550.0078-0.0789-0.0665-44.205523.6527-102.644
101.18960.68050.73510.72080.59311.4476-0.0973-0.14630.0211-0.146-0.08390.16020.0245-0.73490.1812-0.1151-0.1016-0.04120.3388-0.0376-0.073-77.491819.3823-93.8246
1100.16780.16570.16710.16740.4464-0.117-0.0690.0731-0.06980.00530.0194-0.0542-0.23940.1117-0.0978-0.0020.03460.0857-0.0013-0.0709-31.440940.1582-54.3664
121.55060.880.71031.24430.57541.439-0.54570.62750.0213-0.61090.4925-0.2757-0.69110.60740.05320.3805-0.252-0.01520.2478-0.0797-0.1151-23.755652.6899-101.72
131.73980.47910.49530.55610.39012.04330.1893-0.87580.13460.0887-0.38180.21790.2011-1.33050.1925-0.2513-0.34280.05651.315-0.1999-0.1561-93.6920.5721-62.8821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|568 A|601 - A|601 }A5 - 568
2X-RAY DIFFRACTION1{ A|5 - A|568 A|601 - A|601 }A601
3X-RAY DIFFRACTION2{ B|2 - B|433 }B2 - 433
4X-RAY DIFFRACTION3{ C|2 - C|248 }C2 - 248
5X-RAY DIFFRACTION4{ D|5 - D|569 }D5 - 569
6X-RAY DIFFRACTION5{ E|2 - E|433 E|501 - E|501 }E2 - 433
7X-RAY DIFFRACTION5{ E|2 - E|433 E|501 - E|501 }E501
8X-RAY DIFFRACTION6{ F|2 - F|248 }F2 - 248
9X-RAY DIFFRACTION7{ G|7 - G|568 }G7 - 568
10X-RAY DIFFRACTION8{ H|2 - H|433 }H2 - 433
11X-RAY DIFFRACTION9{ I|2 - I|248 }I2 - 248
12X-RAY DIFFRACTION10{ J|6 - J|568 }J6 - 568
13X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }A603 - 606
14X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }B501 - 502
15X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }E502 - 503
16X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }D601 - 602
17X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }G602 - 605
18X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }H501
19X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }K501
20X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }J601 - 602
21X-RAY DIFFRACTION12{ K|2 - K|433 }K2 - 433
22X-RAY DIFFRACTION13{ L|3 - L|248 }L3 - 248

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