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- PDB-5a0y: METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS... -

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Basic information

Entry
Database: PDB / ID: 5a0y
TitleMETHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS AT 1.1 A RESOLUTION
Components(METHYL-COENZYME M REDUCTASE I SUBUNIT ...) 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 / 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 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 / Resolution: 1.1 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
DepositionApr 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 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 2.0Apr 24, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 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_conn_type / 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_conn_type.id / _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 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)276,75833
Polymers273,4296
Non-polymers3,32927
Water50,3342794
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54190 Å2
ΔGint-358.4 kcal/mol
Surface area60610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.227, 118.300, 122.560
Angle α, β, γ (deg.)90.00, 91.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.62712, -0.77707, 0.05374), (-0.77689, -0.62897, -0.02881), (0.05619, -0.02369, -0.99814)40.32626, 79.83562, -65.58157
2given(0.62528, -0.77869, 0.05156), (-0.77847, -0.62702, -0.02893), (0.05486, -0.02205, -0.99825)40.3314, 79.7849, -65.58967
3given(0.62721, -0.77759, 0.04415), (-0.77703, -0.62861, -0.03263), (0.05312, -0.01384, -0.99849)40.2905, 79.78548, -65.77512

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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 / MCR I ALPHA / COENZYME-B SULFOETHYLTHIOTRANSFERASE ALPHA


Mass: 60637.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
Source: (natural) METHANOTHERMOBACTER MARBURGENSIS (archaea)
Strain: MARBURG
References: UniProt: P11558, coenzyme-B sulfoethylthiotransferase
#2: Protein METHYL-COENZYME M REDUCTASE I SUBUNIT BETA / MCR I BETA / COENZYME-B SULFOETHYLTHIOTRANSFERASE BETA


Mass: 47279.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
Source: (natural) METHANOTHERMOBACTER MARBURGENSIS (archaea)
Strain: MARBURG
References: UniProt: P11560, coenzyme-B sulfoethylthiotransferase
#3: Protein METHYL-COENZYME M REDUCTASE I SUBUNIT GAMMA / MCR I GAMMA / COENZYME-B SULFOETHYLTHIOTRANSFERASE GAMMA


Mass: 28797.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
Source: (natural) METHANOTHERMOBACTER MARBURGENSIS (archaea)
Strain: MARBURG
References: UniProt: P11562, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 8 types, 2821 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#6: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


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


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 2794 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsDIDEHYDROASPARTATE (DYA): DIDEHYDROASPARTATE IS AN ASPARTATE CONTAINING A DOUBLE BOND BETWEEN THE C ...DIDEHYDROASPARTATE (DYA): DIDEHYDROASPARTATE IS AN ASPARTATE CONTAINING A DOUBLE BOND BETWEEN THE C ALPHA AND C BETA
Sequence detailsRESIDUE 450 IS A DIDEHYDROASPARTATE

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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: 2.18 Å3/Da / Density % sol: 43.65 % / Description: NONE
Crystal growpH: 9
Details: 27.5% (V/V) PEG 400, 100 MM HEPES PH 7.5, 250 MM MGCL2, AND 200 MM NACL

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.85506
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85506 Å / Relative weight: 1
ReflectionResolution: 1.1→48.35 Å / Num. obs: 937928 / % possible obs: 99.3 % / Observed criterion σ(I): 1.7 / Redundancy: 3.4 % / Biso Wilson estimate: 9.06 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 97.8

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Processing

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

3pot


Resolution: 1.1→48.346 Å / SU ML: 0.1 / σ(F): 1.33 / Phase error: 12.26 / Stereochemistry target values: ML
Details: CONSIDERING THE RESOLUTION HYDROGEN REFINEMENT MODEL HAS BEEN USED WITH THE RIDING MODEL A NEW POST-TRANSLATIONAL MODIFICATION IS PRESENT IN THE CHAIN A AND D CALLED DIDEHYDROASPARTATE AT THE POSITION 450
RfactorNum. reflection% reflection
Rfree0.1291 46957 5 %
Rwork0.1107 --
obs0.1117 937784 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.13 Å2
Refinement stepCycle: LAST / Resolution: 1.1→48.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19135 0 201 2794 22130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01320425
X-RAY DIFFRACTIONf_angle_d1.64927873
X-RAY DIFFRACTIONf_dihedral_angle_d14.137752
X-RAY DIFFRACTIONf_chiral_restr0.0743059
X-RAY DIFFRACTIONf_plane_restr0.0113724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0997-1.11220.29315760.272928143X-RAY DIFFRACTION95
1.1122-1.12530.27115440.24929546X-RAY DIFFRACTION99
1.1253-1.1390.257415190.229929370X-RAY DIFFRACTION99
1.139-1.15340.230915840.212229499X-RAY DIFFRACTION99
1.1534-1.16860.213415640.193429477X-RAY DIFFRACTION99
1.1686-1.18460.207714730.183629571X-RAY DIFFRACTION99
1.1846-1.20150.20415510.178429597X-RAY DIFFRACTION99
1.2015-1.21950.188616220.167429576X-RAY DIFFRACTION99
1.2195-1.23850.177915130.158829641X-RAY DIFFRACTION99
1.2385-1.25880.18416410.156929601X-RAY DIFFRACTION99
1.2588-1.28050.164215170.147829755X-RAY DIFFRACTION99
1.2805-1.30380.167315500.146929687X-RAY DIFFRACTION99
1.3038-1.32890.170916070.137229726X-RAY DIFFRACTION100
1.3289-1.3560.141716040.115429627X-RAY DIFFRACTION100
1.356-1.38550.141615360.113229874X-RAY DIFFRACTION100
1.3855-1.41780.132614930.108529849X-RAY DIFFRACTION100
1.4178-1.45320.122715170.095129811X-RAY DIFFRACTION100
1.4532-1.49250.11615790.08829859X-RAY DIFFRACTION100
1.4925-1.53640.109815640.083129891X-RAY DIFFRACTION100
1.5364-1.5860.109915830.077629867X-RAY DIFFRACTION100
1.586-1.64270.101215570.074629888X-RAY DIFFRACTION100
1.6427-1.70850.097915810.073929887X-RAY DIFFRACTION100
1.7085-1.78620.098516160.075729850X-RAY DIFFRACTION100
1.7862-1.88040.102815880.079829812X-RAY DIFFRACTION100
1.8804-1.99820.106315600.083729970X-RAY DIFFRACTION100
1.9982-2.15250.104316110.087929855X-RAY DIFFRACTION100
2.1525-2.36910.105315600.087429783X-RAY DIFFRACTION99
2.3691-2.71190.107815180.093829795X-RAY DIFFRACTION99
2.7119-3.41660.118215900.109229989X-RAY DIFFRACTION100
3.4166-48.39260.120516390.116330031X-RAY DIFFRACTION99

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