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- PDB-5n28: METHYL-COENZYME M REDUCTASE III FROM METHANOTORRIS FORMICICUS MON... -

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Basic information

Entry
Database: PDB / ID: 5n28
TitleMETHYL-COENZYME M REDUCTASE III FROM METHANOTORRIS FORMICICUS MONOCLINIC FORM
Components
  • (Methyl-coenzyme M reductase, ...) x 2
  • Methyl-coenzyme M reductase subunit alpha
KeywordsTRANSFERASE / POST-TRANSLATIONAL MODIFICATION / BINDING SITES / CATALYSIS / COENZYMES / DISULFIDES / HYDROGEN / HYDROGEN BONDING / LIGANDS / MESNA / METALLOPORPHYRINS / METHANE / METHANOCOCCALES / NICKEL / OXIDATION-REDUCTION / OXIDOREDUCTASES / PHOSPHOTHREONINE / PROTEIN CONFORMATION / PROTEIN FOLDING / PROTEIN STRUCTURE / THERMOPHILE / AUTOTROPH / HYDROXY-TRYPTOPHANE
Function / homology
Function and homology information


coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding
Similarity search - Function
Methyl-coenzyme M Reductase; Chain B, domain 2 / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 1 / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit ...Methyl-coenzyme M Reductase; Chain B, domain 2 / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 1 / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit superfamily / 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 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 / Lambda Exonuclease; Chain A / Alpha-Beta Plaits / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1-THIOETHANESULFONIC ACID / FACTOR 430 / : / Coenzyme B / Methyl-coenzyme M reductase subunit alpha / Methyl-coenzyme M reductase subunit gamma / Methyl-coenzyme M reductase subunit beta
Similarity search - Component
Biological speciesMethanotorris formicicus Mc-S-70 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWagner, T. / Wegner, C.E. / Ermler, U. / Shima, S.
CitationJournal: J.Bacteriol. / Year: 2017
Title: Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales.
Authors: Wagner, T. / Wegner, C.E. / Kahnt, J. / Ermler, U. / Shima, S.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume / _citation.title
Revision 1.2Jan 17, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)280,81713
Polymers277,9946
Non-polymers2,8237
Water50428
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55510 Å2
ΔGint-284 kcal/mol
Surface area62020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.680, 81.160, 154.950
Angle α, β, γ (deg.)90.00, 107.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Methyl-coenzyme M reductase subunit alpha


Mass: 61180.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: IN CHAIN A AND D RESIDUE 260 IS A N1-METHYLHISTIDINE. RESIDUE 274 IS A C5-(S)-METHYLARGININE. RESIDUE 402 IS A C2-(S)-METHYLGLUTAMINE. RESIDUE 429 IS A POSSIBLE 6-HYDROXY-TRYPTOPHANE. ...Details: IN CHAIN A AND D RESIDUE 260 IS A N1-METHYLHISTIDINE. RESIDUE 274 IS A C5-(S)-METHYLARGININE. RESIDUE 402 IS A C2-(S)-METHYLGLUTAMINE. RESIDUE 429 IS A POSSIBLE 6-HYDROXY-TRYPTOPHANE. RESIDUE 447 IS A THIOGLYCINE.
Source: (natural) Methanotorris formicicus Mc-S-70 (archaea)
Cell line: / / Organ: / / Plasmid details: DSMZ / Variant: Wild-type / Tissue: /
References: UniProt: H1KXL5, coenzyme-B sulfoethylthiotransferase

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Methyl-coenzyme M reductase, ... , 2 types, 4 molecules BECF

#2: Protein Methyl-coenzyme M reductase, beta subunit


Mass: 47541.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanotorris formicicus Mc-S-70 (archaea)
Cell line: / / Organ: / / Plasmid details: DSMZ / Variant: Wild-type / Tissue: /
References: UniProt: H1KXL9, coenzyme-B sulfoethylthiotransferase
#3: Protein Methyl-coenzyme M reductase, gamma subunit


Mass: 30274.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanotorris formicicus Mc-S-70 (archaea)
Cell line: / / Organ: / / Plasmid details: DSMZ / Variant: Wild-type / Tissue: /
References: UniProt: H1KXL6, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 5 types, 35 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


Mass: 343.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO7PS
#6: Chemical ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.27 Å3/Da / Density % sol: 45.8 % / Description: Yellow rod-shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 ul of MCR III from M. formicicus (35 mg/ml) and 1 ul of reservoir solution containing 20% PEG 8000 (w/v), 100 mM MES pH 7.0. The cryoprotection solution contains 20% PEG 8000 (w/v), 100 mM ...Details: 2 ul of MCR III from M. formicicus (35 mg/ml) and 1 ul of reservoir solution containing 20% PEG 8000 (w/v), 100 mM MES pH 7.0. The cryoprotection solution contains 20% PEG 8000 (w/v), 100 mM MES pH 7.0, 25% ethylene glycol (v/v).
PH range: / / Temp details: /

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.8→49.36 Å / Num. obs: 60676 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 79.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.05 / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8783 / Num. unique obs: 8783 / CC1/2: 0.317 / Rpim(I) all: 0.371 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MCRII from Methanothermobacter wolfeii PDB:5A8W

5a8w


Resolution: 2.8→48.43 Å / Cor.coef. Fo:Fc: 0.9471 / Cor.coef. Fo:Fc free: 0.9445 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.312
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 3016 4.97 %RANDOM
Rwork0.1931 ---
obs0.1936 60657 99.9 %-
Displacement parametersBiso mean: 94.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.9682 Å20 Å2-2.6958 Å2
2--1.3006 Å20 Å2
3----2.2688 Å2
Refine analyzeLuzzati coordinate error obs: 0.477 Å
Refinement stepCycle: 1 / Resolution: 2.8→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19266 0 181 28 19475
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00819978HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0527112HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6977SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes505HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2927HARMONIC5
X-RAY DIFFRACTIONt_it19978HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion17.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2583SEMIHARMONIC5
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_contact23466SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2487 214 4.8 %
Rwork0.2544 4243 -
all0.2541 4457 -
obs--99.9 %
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)
10.99590-0.13840.25260.28170.86360.03750.0479-0.0808-0.3227-0.0285-0.21910.06710.233-0.0090.10620.11350.1711-0.1161-0.01910.15039.1327-9.368131.9878
21.2661-0.01860.35280.5940.46441.1055-0.0131-0.19380.03450.1127-0.1424-0.0626-0.0371-0.07530.1555-0.04770.0604-0.0107-0.00820.04660.0718-14.75734.607861.3891
34.2022.73170.04031.41010.27010.2444-0.0101-0.05990.04630.01180.0302-0.0462-0.09620.1277-0.0202-0.1472-0.0848-0.0877-0.0034-0.03750.097218.750915.130561.487
41.10240.04550.33610.3301-0.20650.45330.04350.2130.0973-0.2186-0.0836-0.1386-0.1641-0.15870.04010.20760.1170.1541-0.07370.0881-0.0322-16.64299.483418.3104
50.94750.05490.55940.80280.09580.5907-0.01530.0347-0.12520.0102-0.1379-0.01130.1413-0.2420.1532-0.0507-0.06390.1070.0168-0.070.1401-31.9701-18.974342.5714
61.47160.34892.40261.59381.55013.9202-0.01030.0711-0.0962-0.08280.00350.07080.1158-0.08540.00670.1273-0.0079-0.06170.1648-0.15510.024-40.7687-20.30559.2841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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