[English] 日本語
Yorodumi
- PDB-5a8k: METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER WOLFEII AT 1... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

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

#1: Protein METHYL-COENZYME M REDUCTASE / Coenzyme-B sulfoethylthiotransferase


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 / Coenzyme-B sulfoethylthiotransferase


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 / Coenzyme-B sulfoethylthiotransferase


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

-
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 / Coenzyme B


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 / Cofactor F430


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


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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more