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- PDB-5n1q: METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLI... -

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Basic information

Entry
Database: PDB / ID: 5n1q
TitleMETHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS AT 1.9 A RESOLUTION
Components(METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ...) x 3
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
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; 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 beta / Methyl-coenzyme M reductase subunit gamma
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume / _citation.title
Revision 1.2May 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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 III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ALPHA
B: METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT BETA
C: METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT GAMMA
D: METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ALPHA
E: METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT BETA
F: METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,97517
Polymers277,8516
Non-polymers3,12411
Water23,1131283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56960 Å2
ΔGint-294 kcal/mol
Surface area62840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.811, 77.224, 145.458
Angle α, β, γ (deg.)90.00, 107.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ... , 3 types, 6 molecules ADBECF

#1: Protein METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ALPHA


Mass: 61194.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: IN CHAIN A, D RESIDUE 261 IS A N1-METHYLHISTIDINE. RESIDUE 275 IS A C5-(S)-METHYLARGININE. RESIDUE 403 IS A C2-(S)-METHYLGLUTAMINE. RESIDUE 448 IS A THIOGLYCINE.
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Plasmid details: DSMZ
References: UniProt: A0A247D6X3*PLUS, coenzyme-B sulfoethylthiotransferase
#2: Protein METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT BETA


Mass: 47362.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Plasmid details: DSMZ
References: UniProt: A0A247D6X4*PLUS, coenzyme-B sulfoethylthiotransferase
#3: Protein METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT GAMMA


Mass: 30368.537 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Plasmid details: DSMZ
References: UniProt: A0A247D6X5*PLUS, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 7 types, 1294 molecules

#4: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


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


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


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


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1283 / 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: 2.19 Å3/Da / Density % sol: 43.8 % / Description: Yellow brick
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 1 ul of MCR III from M. thermolithotrophicus with a concentration of 35 mg/ml was mixed with 1 ul of reservoir solution. Best crystals with a yellow brick morphology appeared after a few ...Details: 1 ul of MCR III from M. thermolithotrophicus with a concentration of 35 mg/ml was mixed with 1 ul of reservoir solution. Best crystals with a yellow brick morphology appeared after a few days in 19% (w/v) polyethylene glycol 3350 and 200 mM MgCl2 in the absence of buffer. The crystals were immersed in a solution containing 19% (w/v) PEG 3350 and 200 mM MgCl2, 30% glycerol (v/v) prior to freezing in liquid nitrogen.
Temp details: grow between 290 - 293 Kelvin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99979 Å / Relative weight: 1
ReflectionResolution: 1.9→46.36 Å / Num. obs: 185011 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.92 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.053 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 26774 / CC1/2: 0.804 / Rpim(I) all: 0.346 / % possible all: 98.7

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.6.22data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MCR III from Methanotorris formicicus

Resolution: 1.9→45.63 Å / Cor.coef. Fo:Fc: 0.9567 / Cor.coef. Fo:Fc free: 0.9485 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.147 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 9074 4.91 %RANDOM
Rwork0.1693 ---
obs0.1704 184823 98.96 %-
Displacement parametersBiso mean: 35.43 Å2
Baniso -1Baniso -2Baniso -3
1-7.0358 Å20 Å21.753 Å2
2---4.8394 Å20 Å2
3----2.1964 Å2
Refine analyzeLuzzati coordinate error obs: 0.229 Å
Refinement stepCycle: 1 / Resolution: 1.9→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19352 0 1557 1283 22192
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00920034HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0427172HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7051SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes515HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2938HARMONIC5
X-RAY DIFFRACTIONt_it20034HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion16.83
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_contact23836SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 660 4.91 %
Rwork0.2481 12769 -
all0.2485 13429 -
obs--98.96 %
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)
10.4479-0.09060.11550.1425-0.13050.22540.0443-0.1635-0.1197-0.01650.02770.06130.1059-0.1023-0.0720.0059-0.0416-0.0353-0.01240.0518-0.038213.8942-16.338838.8052
20.892-0.01630.33710.1495-0.0970.1766-0.00670.04530.1778-0.0411-0.02190.0348-0.0114-0.00270.02860.0218-0.0205-0.0147-0.03970.01-0.032625.347512.343712.5009
30.4722-0.3107-0.14380.1889-0.00950.27530.0016-0.13160.1078-0.07990.09830.0583-0.0105-0.0593-0.0999-0.0563-0.0082-0.0188-0.0188-0.03520.025-7.364914.354725.4669
40.46580.06890.08610.1774-0.04940.14170.0244-0.25470.05260.0445-0.0226-0.0311-0.0340.0151-0.0018-0.0053-0.0268-0.02830.0523-0.0021-0.095940.78561.486652.0877
50.78360.06680.1070.01060.03280.12690.08440.0846-0.1131-0.045-0.0319-0.04580.09290.0684-0.05250.05130.0064-0.0292-0.0529-0.0105-0.050350.3814-11.966215.0136
60.1259-0.0391-0.19140.7507-0.0167-0.09360.0292-0.12860.0031-0.0530.0421-0.06110.06960.1004-0.07130.049-0.0038-0.1365-0.07140.0761-0.065569.7207-23.444642.0928
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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