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- PDB-1hbu: METHYL-COENZYME M REDUCTASE IN THE MCR-RED1-SILENT STATE IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 1hbu
TitleMETHYL-COENZYME M REDUCTASE IN THE MCR-RED1-SILENT STATE IN COMPLEX with COENZYME M
Components(METHYL-COENZYME M REDUCTASE I ...) 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1May 20, 2015Group: Derived calculations / Non-polymer description / Version format compliance
Revision 2.0Jun 21, 2017Group: Advisory / Atomic model / Category: atom_site / pdbx_unobs_or_zero_occ_atoms
Revision 2.1Jul 5, 2017Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 2.2Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
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_alt_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_alt_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 / _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 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)277,10248
Polymers272,6466
Non-polymers4,45642
Water38,4802136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.100, 116.500, 121.800
Angle α, β, γ (deg.)90.00, 91.80, 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 MARBURGENSIS (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 MARBURGENSIS (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 MARBURGENSIS (archaea)
Strain: MARBURG / References: UniProt: P11562

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Non-polymers , 9 types, 2178 molecules

#4: Chemical ChemComp-F43 / FACTOR 430


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


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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#10: Chemical
ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 2136 / Source method: isolated from a natural source / Formula: H2O

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Details

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 RU200 / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 167654 / % possible obs: 94.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.053 / Rsym value: 0.06 / Net I/σ(I): 19.3
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 2 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.17 / % possible all: 61.8
Reflection
*PLUS
Lowest resolution: 10 Å
Reflection shell
*PLUS
% possible obs: 61.8 %

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Processing

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

1mro


Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 -5 %RANDOM
Rwork0.162 ---
obs-167654 94.3 %-
Displacement parametersBaniso 23: 0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19118 0 271 2136 21525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d2.7
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: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS

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