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- PDB-5g0r: METHYL-COENZYME M REDUCTASE I FROM METHANOTHERMOBACTER MARBURGENS... -

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Basic information

Entry
Database: PDB / ID: 5g0r
TitleMETHYL-COENZYME M REDUCTASE I FROM METHANOTHERMOBACTER MARBURGENSIS EXPOSED TO 3-NITROOXYPROPANOL
Components(METHYL-COENZYME M REDUCTASE I SUBUNIT ...) x 3
KeywordsTRANSFERASE / METHYL-COENZYMEM / METHYL-COENZYMEM REDUCTASE EXPOSED TO 3-NITROOXYPROPANOL / POSTTRANSLATIONAL MODIFICATION / BINDING SITES / CATALYSIS / COENZYMES / DISULFIDES / HYDROGEN / LIGANDS / MESNA / METALLOPORPHYRINS / METHANE / METHANOBACTERIUM / NICKEL / OXIDATION-REDUCTION / OXDOREDUCTASES / PHOSPHOTHREONINE / THIOGLYCINE / 3- NITROOXYPROPANOL / INHIBITOR / GREENHOUSE GAS
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
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: 1.25 Å
AuthorsWagner, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mode of Action Uncovered for the Specific Reduction of Methane Emissions from Ruminants by the Small Molecule 3-Nitrooxypropanol.
Authors: Duin, E.C. / Wagner, T. / Shima, S. / Prakash, D. / Cronin, B. / Yanez-Ruiz, D.R. / Duval, S. / Rumbeli, R. / Stemmler, R.T. / Thauer, R.K. / Kindermann, M.
History
DepositionMar 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jun 15, 2016Group: Database references
Revision 1.4Mar 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 2.1May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 2.2Jan 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_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 / _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)276,58135
Polymers273,4296
Non-polymers3,15229
Water47,0012609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54180 Å2
ΔGint-394.5 kcal/mol
Surface area60600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.200, 118.101, 122.640
Angle α, β, γ (deg.)90.00, 92.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.63003, -0.77475, 0.05315), (-0.77461, -0.63183, -0.02782), (0.05514, -0.02365, -0.9982)40.06858, 79.7606, -65.56581
2given(0.62836, -0.77619, 0.05182), (-0.77603, -0.63008, -0.02781), (0.05424, -0.02274, -0.99827)40.12504, 79.75369, -65.5992
3given(0.62887, -0.77613, 0.04635), (-0.77578, -0.63033, -0.02905), (0.05176, -0.01769, -0.9985)40.10783, 79.74027, -65.68895

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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 / METHYL-COENZYME M REDUCTASE


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 / METHYL-COENZYME M REDUCTASE


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 / METHYL-COENZYME M REDUCTASE


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 , 7 types, 2638 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / 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-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO7PS
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2609 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 43.6 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 25-28 % V/V PEG 400, 300 MM MGCL2, 200 MM NACL AND 100 MM HEPES PH 7.5 CRYSTAL GROWTH AT 8 DEGREE CELSIUS UNDER AEROBIC CONDITION

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97128
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97128 Å / Relative weight: 1
ReflectionResolution: 1.25→38.79 Å / Num. obs: 633330 / % possible obs: 98.5 % / Observed criterion σ(I): 4 / Redundancy: 4.6 % / Biso Wilson estimate: 9.86 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.4 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A0Y

5a0y


Resolution: 1.25→38.795 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 10.8 / Stereochemistry target values: ML
Details: CONSIDERING THE RESOLUTION HYDROGEN REFINEMENT MODEL HAS BEEN USED WITH THE RIDING MODE THE INHIBITOR 3-NITROOXYPROPANOL HAS POSSIBLY REDUCED THE NICKEL CENTER AND IS NOW HYDROLYSED IN THE ...Details: CONSIDERING THE RESOLUTION HYDROGEN REFINEMENT MODEL HAS BEEN USED WITH THE RIDING MODE THE INHIBITOR 3-NITROOXYPROPANOL HAS POSSIBLY REDUCED THE NICKEL CENTER AND IS NOW HYDROLYSED IN THE ACTIVE SITE. SINCE THERE IS A LOW PARTIAL OCCUPANCY OF THE BROKEN COMPOUND (NITRITE AND 1-3-PROPANEDIOL) IN THE ACTIVE SITE, WATER MOLECULE HAVE BEEN PLACED INSTEAD.
RfactorNum. reflection% reflection
Rfree0.1237 31689 5 %
Rwork0.1052 --
obs0.1062 633010 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.54 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19135 0 191 2609 21935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01220400
X-RAY DIFFRACTIONf_angle_d1.52227838
X-RAY DIFFRACTIONf_dihedral_angle_d14.0487735
X-RAY DIFFRACTIONf_chiral_restr0.0683053
X-RAY DIFFRACTIONf_plane_restr0.013724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2499-1.26410.167910150.138719961X-RAY DIFFRACTION98
1.2641-1.2790.164410660.132719852X-RAY DIFFRACTION98
1.279-1.29460.156910380.130419921X-RAY DIFFRACTION98
1.2946-1.3110.156910620.126219917X-RAY DIFFRACTION98
1.311-1.32820.148810180.122119865X-RAY DIFFRACTION98
1.3282-1.34640.14859860.11719846X-RAY DIFFRACTION97
1.3464-1.36570.139810730.110820068X-RAY DIFFRACTION99
1.3657-1.38610.142110810.1120031X-RAY DIFFRACTION99
1.3861-1.40770.143811290.108319927X-RAY DIFFRACTION98
1.4077-1.43080.13710440.102219957X-RAY DIFFRACTION98
1.4308-1.45550.129210580.097719994X-RAY DIFFRACTION98
1.4555-1.48190.132310270.098620012X-RAY DIFFRACTION99
1.4819-1.51040.129610600.096120063X-RAY DIFFRACTION99
1.5104-1.54130.126810040.093819865X-RAY DIFFRACTION98
1.5413-1.57480.11819900.091619899X-RAY DIFFRACTION97
1.5748-1.61140.11510040.0920190X-RAY DIFFRACTION99
1.6114-1.65170.126710790.091820126X-RAY DIFFRACTION99
1.6517-1.69640.122510590.091220068X-RAY DIFFRACTION99
1.6964-1.74630.113910530.090520098X-RAY DIFFRACTION99
1.7463-1.80270.117710690.096820089X-RAY DIFFRACTION99
1.8027-1.86710.126310690.101120153X-RAY DIFFRACTION99
1.8671-1.94180.1210390.101719771X-RAY DIFFRACTION97
1.9418-2.03020.120210980.100620111X-RAY DIFFRACTION99
2.0302-2.13720.114210610.096420199X-RAY DIFFRACTION99
2.1372-2.27110.108911730.093720152X-RAY DIFFRACTION99
2.2711-2.44650.112810580.094220084X-RAY DIFFRACTION99
2.4465-2.69260.114210880.100820082X-RAY DIFFRACTION98
2.6926-3.08210.120510490.112120148X-RAY DIFFRACTION99
3.0821-3.88250.124110860.115420429X-RAY DIFFRACTION100
3.8825-38.81360.122210530.118120443X-RAY DIFFRACTION99

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