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- PDB-1hbm: METHYL-COENZYME M REDUCTASE ENZYME PRODUCT COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1hbm
TitleMETHYL-COENZYME M REDUCTASE ENZYME PRODUCT COMPLEX
Components(METHYL-COENZYME M REDUCTASE I ...Coenzyme-B sulfoethylthiotransferase) x 3
KeywordsMETHANOGENESIS / BIOLOGICAL METHANOGENESIS / NI-ENZYME / OXIDOREDUCTASE
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 / 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, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit ...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, alpha subunit, N-terminal subdomain 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
FACTOR 430 / Chem-SHT / 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 THERMAUTOTROPHICUS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsErmler, U. / Grabarse, W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: On the Mechanism of Biological Methane Formation: Structural Evidence for Conformational Changes in Methyl-Coenzyme M Reductase Upon Substrate Binding
Authors: Grabarse, W. / Mahlert, F. / Duin, E.C. / Goubeaud, M. / Shima, S. / Thauer, R.K. / Lamzin, V. / Ermler, U.
History
DepositionApr 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: 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
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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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 ALPHA SUBUNIT
B: METHYL-COENZYME M REDUCTASE I BETA SUBUNIT
C: METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT
D: METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT
E: METHYL-COENZYME M REDUCTASE I BETA SUBUNIT
F: METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,90038
Polymers272,6466
Non-polymers4,25432
Water37,6872092
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.000, 118.300, 122.800
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6268, -0.7779, 0.0458), (-0.7781, -0.6279, -0.0171), (0.0421, -0.0249, -0.9988)
Vector: 39.8417, 79.4824, -65.4262)

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Components

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

#1: Protein METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT


Mass: 60508.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: MARBURG / References: UniProt: P11558
#2: Protein METHYL-COENZYME M REDUCTASE I BETA SUBUNIT


Mass: 47148.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: MARBURG / References: UniProt: P11560
#3: Protein METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT


Mass: 28666.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: MCR-OX-SILENT STATE, ENZYME-SUBSTRATE COMPLEX
Source: (natural) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Cellular location: CYTOPLASM / Strain: MARBURG / References: UniProt: P11562

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Non-polymers , 8 types, 2124 molecules

#4: Chemical ChemComp-F43 / FACTOR 430 / Cofactor F430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#5: Chemical ChemComp-SHT / O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE


Mass: 481.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H24NO10PS3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2092 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYZES THE FINAL STEP IN METHANOGENESIS, THE TERMINAL STEP OF ANAEROBIC DEGRADATION OF BIOMASS.
Sequence detailsREFERENCE: 1 RESIDUE IS LACKING IN THE C-TERMINUS AND THE N-TERMINUS, C AND N-TERMINUS ARE VISIBLE ...REFERENCE: 1 RESIDUE IS LACKING IN THE C-TERMINUS AND THE N-TERMINUS, C AND N-TERMINUS ARE VISIBLE IN THE CRYSTAL STRUCTURE. MET 1 WAS CLEARLY SHOWN NOT TO BE PRESENT.

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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: 3.9 Å3/Da / Density % sol: 31 %
Crystal growpH: 7.5
Details: 25% PEG 400, 0.2 M NACL, 20 MG/ML FINAL PROTEIN CONC, 0.2 M MGCL, 0.1 M HEPES PH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-25 %PEG4001reservoir
2200 mM1reservoirNaCl
3200 mM1reservoirMgCl2
4100 mMTris-HCl1reservoir
520 %(w/w)glycerol1reservoir
650 mg/mlprotein1drop
710 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 198635 / % possible obs: 91.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.088 / Rsym value: 0.08 / Net I/σ(I): 8.21
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.19 / % possible all: 74.9
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 74.9 % / Rmerge(I) obs: 0.183

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MRO

1mro


Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.193 -5 %RANDOM
Rwork0.164 ---
obs-198635 91.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19112 0 263 2092 21467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.2
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS

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