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- PDB-5a8k: METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER WOLFEII AT 1... -

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Basic information

Entry
Database: PDB / ID: 5a8k
TitleMETHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER WOLFEII AT 1.4 A RESOLUTION
Components(METHYL-COENZYME M ...) x 3
KeywordsTRANSFERASE / POST-TRANSLATIONAL MODIFICATION / BINDING SITES / CATALYSIS / COENZYMES / DISULFIDES / HYDROGEN / HYDROGEN BONDING / LIGANDS / MESNA / METALLOPORPHYRINS / METHANE / METHANOBACTERIUM / MODELS / MOLECULAR / NICKEL / OXIDATION-REDUCTION / OXIDOREDUCTASES / PHOSPHOTHREONINE / PROTEIN CONFORMATION / PROTEIN FOLDING / PROTEIN STRUCTURE
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 / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 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; Chain B, domain 2 / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 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 / 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 / 2-ETHOXYETHANOL / FACTOR 430 / : / Coenzyme B / Methyl-coenzyme M reductase subunit beta / Methyl-coenzyme M reductase subunit gamma / coenzyme-B sulfoethylthiotransferase
Similarity search - Component
Biological speciesMETHANOTHERMOBACTER WOLFEII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsWagner, T. / Ermler, U.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation.
Authors: Wagner, T. / Kahnt, J. / Ermler, U. / Shima, S.
History
DepositionJul 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Mar 29, 2017Group: Non-polymer description
Revision 1.4May 15, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_label_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
B: METHYL-COENZYME M REDUCTASE
C: METHYL-COENZYME M REDUCTASE
D: METHYL-COENZYME M REDUCTASE
E: METHYL-COENZYME M REDUCTASE
F: METHYL-COENZYME M REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,26556
Polymers273,4376
Non-polymers5,82850
Water44,3532462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60860 Å2
ΔGint-246.5 kcal/mol
Surface area60430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.140, 150.540, 187.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.13547, -0.98206, 0.13116), (-0.98241, -0.15031, -0.11077), (0.1285, -0.11384, -0.98515)40.98948, 50.71066, 25.09539
2given(0.13274, -0.98244, 0.13111), (-0.98248, -0.14788, -0.11342), (0.13082, -0.11375, -0.98486)41.17384, 50.74581, 25.05123
3given(0.13576, -0.98181, 0.13275), (-0.98263, -0.15054, -0.10851), (0.12652, -0.11572, -0.98519)40.83729, 50.66264, 25.28807

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Components

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METHYL-COENZYME M ... , 3 types, 6 molecules ADBECF

#1: Protein METHYL-COENZYME M REDUCTASE


Mass: 60666.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) METHANOTHERMOBACTER WOLFEII (archaea)
References: UniProt: H7CHY1*PLUS, coenzyme-B sulfoethylthiotransferase
#2: Protein METHYL-COENZYME M REDUCTASE


Mass: 47324.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) METHANOTHERMOBACTER WOLFEII (archaea)
References: UniProt: A0A1C7D1E2*PLUS, coenzyme-B sulfoethylthiotransferase
#3: Protein METHYL-COENZYME M REDUCTASE


Mass: 28727.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) METHANOTHERMOBACTER WOLFEII (archaea)
References: UniProt: A0A1C7D1E3*PLUS, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 8 types, 2512 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#9: Chemical...
ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C4H10O2
#10: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2462 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMETHANOTHERMOBACTER WOLFEII GENOME SEQUENCING IS ACTUALLY IN PROGRESS AND WILL BE RELEASED SOON. ...METHANOTHERMOBACTER WOLFEII GENOME SEQUENCING IS ACTUALLY IN PROGRESS AND WILL BE RELEASED SOON. THE SEQUENCE OF THIS STRUCTURE HAS BEEN CONFIRMED BY THE EARLY SEQUENCED INFORMATION

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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: 2.17 Å3/Da / Density % sol: 43.35 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 37% (V/V) 2-ETHOXYETHANOL, 50 MM CALCIUM ACETATE, AND 100 MM HEPES PH 7.0 AT 8 DEGREE CELSIUS

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97798
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97798 Å / Relative weight: 1
ReflectionResolution: 1.41→48.47 Å / Num. obs: 453580 / % possible obs: 99.9 % / Observed criterion σ(I): 2.8 / Redundancy: 8 % / Biso Wilson estimate: 10.09 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.7
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3POT

3pot


Resolution: 1.41→48.467 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 12.31 / Stereochemistry target values: ML
Details: CONSIDERING THE RESOLUTION HYDROGEN REFINEMENT MODEL HAS BEEN USED WITH THE RIDING MODE
RfactorNum. reflection% reflection
Rfree0.1397 22739 5 %
Rwork0.1138 --
obs0.1151 453249 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.028 Å2
Refinement stepCycle: LAST / Resolution: 1.41→48.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19135 0 354 2462 21951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0120302
X-RAY DIFFRACTIONf_angle_d1.41227603
X-RAY DIFFRACTIONf_dihedral_angle_d14.3377692
X-RAY DIFFRACTIONf_chiral_restr0.0583018
X-RAY DIFFRACTIONf_plane_restr0.0083663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.4260.22337690.181114286X-RAY DIFFRACTION100
1.426-1.44280.23487470.186914165X-RAY DIFFRACTION100
1.4428-1.46040.21677520.179114255X-RAY DIFFRACTION100
1.4604-1.47890.23467170.188514266X-RAY DIFFRACTION100
1.4789-1.49840.18237550.138114271X-RAY DIFFRACTION100
1.4984-1.51890.18747500.142414194X-RAY DIFFRACTION100
1.5189-1.54060.18747680.148514216X-RAY DIFFRACTION100
1.5406-1.56360.17147560.124814252X-RAY DIFFRACTION100
1.5636-1.5880.15357430.115314323X-RAY DIFFRACTION100
1.588-1.6140.15587600.110214262X-RAY DIFFRACTION100
1.614-1.64190.14847360.105914316X-RAY DIFFRACTION100
1.6419-1.67170.14427570.103114238X-RAY DIFFRACTION100
1.6717-1.70390.14068160.097314212X-RAY DIFFRACTION100
1.7039-1.73870.14627240.102714284X-RAY DIFFRACTION100
1.7387-1.77650.13277470.097414322X-RAY DIFFRACTION100
1.7765-1.81780.13697700.096914307X-RAY DIFFRACTION100
1.8178-1.86330.13238000.100314226X-RAY DIFFRACTION100
1.8633-1.91360.13767460.111514349X-RAY DIFFRACTION100
1.9136-1.970.14737390.112614302X-RAY DIFFRACTION100
1.97-2.03350.12897850.099714327X-RAY DIFFRACTION100
2.0335-2.10620.12837200.104714375X-RAY DIFFRACTION100
2.1062-2.19060.12047840.09214307X-RAY DIFFRACTION100
2.1906-2.29030.12627590.098614372X-RAY DIFFRACTION100
2.2903-2.4110.11457360.092814411X-RAY DIFFRACTION100
2.411-2.5620.1187720.095414439X-RAY DIFFRACTION100
2.562-2.75980.12267970.101414368X-RAY DIFFRACTION100
2.7598-3.03750.12437620.109114507X-RAY DIFFRACTION100
3.0375-3.4770.13747800.123714563X-RAY DIFFRACTION100
3.477-4.38020.11817230.107714694X-RAY DIFFRACTION100
4.3802-48.49560.14637690.137315101X-RAY DIFFRACTION100

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