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- PDB-1e6y: Methyl-coenzyme M reductase from Methanosarcina barkeri -

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Basic information

Entry
Database: PDB / ID: 1e6y
TitleMethyl-coenzyme M reductase from Methanosarcina barkeri
Components
  • (METHYL-COENZYME M REDUCTASE SUBUNIT ...Coenzyme-B sulfoethylthiotransferase) x 2
  • METHYL-COENZYME M REDUCTASE I BETA SUBUNIT
KeywordsOXIDOREDUCTASE / BIOLOGICAL METHANOGENESIS / NI-ENZYME / NI ENZYME
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
1-THIOETHANESULFONIC ACID / FACTOR 430 / Coenzyme B / Methyl-coenzyme M reductase subunit beta / Methyl-coenzyme M reductase subunit alpha / Methyl-coenzyme M reductase subunit gamma
Similarity search - Component
Biological speciesMETHANOSARCINA BARKERI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGrabarse, W. / Ermler, U.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Comparison of Three Methyl-Coenzyme M Reductases from Phylogenetically Distant Organisms: Unusual Amino Acid Modification, Conservation and Adaptation
Authors: Grabarse, W. / Mahlert, F. / Shima, S. / Thauer, R.K. / Ermler, U.
History
DepositionAug 23, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 20, 2015Group: Non-polymer description
Revision 1.3Mar 29, 2017Group: Advisory / Non-polymer description
Revision 1.4Oct 17, 2018Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_sheet_hbond ...diffrn_source / pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_sheet_hbond.range_1_auth_atom_id ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.sheet_id
Revision 1.5Jul 10, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7May 4, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.8Dec 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)273,15915
Polymers270,0986
Non-polymers3,0619
Water39,5432195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54880 Å2
ΔGint-246.9 kcal/mol
Surface area57530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.678, 153.099, 153.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.997, 0.0021, -0.0779), (-0.9997, -0.0239), (-0.078, -0.0238, 0.9967)
Vector: 117.3238, 154.28999, 6.4303)

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Components

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METHYL-COENZYME M REDUCTASE SUBUNIT ... , 2 types, 4 molecules ADCF

#1: Protein METHYL-COENZYME M REDUCTASE SUBUNIT ALPHA / Coenzyme-B sulfoethylthiotransferase / COENZYME-B SULFOETHYLTHIOTRANSFERASE ALPHA / METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT


Mass: 61951.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) METHANOSARCINA BARKERI (archaea) / Cellular location: CYTOPLASM
References: UniProt: P07962, coenzyme-B sulfoethylthiotransferase
#3: Protein METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA / Coenzyme-B sulfoethylthiotransferase / METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT / COENZYME-B SULFOETHYLTHIOTRANSFERASE GAMMA


Mass: 27769.170 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) METHANOSARCINA BARKERI (archaea) / Cellular location: CYTOPLASM
References: UniProt: P07964, coenzyme-B sulfoethylthiotransferase

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Protein , 1 types, 2 molecules BE

#2: Protein METHYL-COENZYME M REDUCTASE I BETA SUBUNIT / METHYL-COENZYME M REDUCTASE I BETA SUBUNIT / COENZYME-B SULFOETHYLTHIOTRANSFERASE BETA


Mass: 45328.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) METHANOSARCINA BARKERI (archaea) / Cellular location: CYTOPLASM
References: UniProt: P07955, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 5 types, 2204 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-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE / Coenzyme B


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2195 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE HEXAMER OF TWO ALPHA, TWO BETA, AND TWO GAMMA CHAINS CATALYZES THE FINAL STEP IN ...THE HEXAMER OF TWO ALPHA, TWO BETA, AND TWO GAMMA CHAINS CATALYZES THE FINAL STEP IN METHANOGENESIS, WHICH IS THE TERMINAL STEP OF ANAEROBIC DEGRADATION OF BIOMASS

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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: 2.47 Å3/Da / Density % sol: 39 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
210 mMTris-HCl1drop
310 %(w/v)mPEG50001reservoir
410 %(w/v)2-propanol1reservoir
50.2 Mammonium acetate1reservoir
60.1 Mmagnesium acetate1reservoir
720 %(w/v)glycerol1reservoir
80.1 MMES/KOH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 326507 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.2
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 5.3 / % possible all: 92.3
Reflection shell
*PLUS
% possible obs: 92.3 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MRO

1mro


Resolution: 1.6→30 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 4119399.53 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.179 15708 5 %RANDOM
Rwork0.16 ---
obs0.16 311702 89 %-
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å20 Å20 Å2
2---7.04 Å20 Å2
3---3.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18915 0 198 2195 21308
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.541.5
X-RAY DIFFRACTIONc_mcangle_it0.852
X-RAY DIFFRACTIONc_scbond_it0.972
X-RAY DIFFRACTIONc_scangle_it1.462.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 2408 5 %
Rwork0.227 45831 -
obs--83.4 %
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.06

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