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- PDB-1e6v: Methyl-coenzyme M reductase from Methanopyrus kandleri -

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Basic information

Entry
Database: PDB / ID: 1e6v
TitleMethyl-coenzyme M reductase from Methanopyrus kandleri
Components(METHYL-COENZYME M REDUCTASE I ...Coenzyme-B sulfoethylthiotransferase) x 3
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 gamma / Methyl-coenzyme M reductase I subunit alpha
Similarity search - Component
Biological speciesMETHANOPYRUS KANDLERI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.1May 20, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Mar 29, 2017Group: Non-polymer description
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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_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)282,24012
Polymers279,4566
Non-polymers2,7846
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53570 Å2
ΔGint-280.86 kcal/mol
Surface area60210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.519, 115.740, 268.510
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: (-0.9285, -0.0103, -0.3713), (-0.0099, -0.9986, 0.0525), (-0.3713, 0.0524, 0.927)
Vector: 147.0659, -34.9694, 29.2869)

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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: 61398.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) METHANOPYRUS KANDLERI (archaea) / Cellular location: CYTOPLASMA / References: UniProt: Q49605
#2: Protein METHYL-COENZYME M REDUCTASE I BETA SUBUNIT


Mass: 48214.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) METHANOPYRUS KANDLERI (archaea) / Cellular location: CYTOPLASMA / References: UniProt: Q49601
#3: Protein METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT


Mass: 30114.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) METHANOPYRUS KANDLERI (archaea) / Cellular location: CYTOPLASMA / References: UniProt: Q49604

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Non-polymers , 3 types, 6 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

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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: 2.24 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: 30.8 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: 1MRO

1mro


Resolution: 2.7→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 274750.55 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED, REFINEMENT WAS CARRIED WITH NCS RESTRAINTS AND THE PDB GENERATED THE ATOMS FOR CHAINS D, E, F. MCR FROM M. KANDLERI MIGHT CONTAIN MODIFIED AMINO ACIDS ANALOGOUS TO ...Details: BULK SOLVENT MODEL USED, REFINEMENT WAS CARRIED WITH NCS RESTRAINTS AND THE PDB GENERATED THE ATOMS FOR CHAINS D, E, F. MCR FROM M. KANDLERI MIGHT CONTAIN MODIFIED AMINO ACIDS ANALOGOUS TO MCR FROM M. THERMOAUTOTROPHICUM AND M. BARKERI. THE DATA SET IS OF UNUSUALLY LOW COMPLETENESS CORRESPONDING TO ABOUT 3.2 A EFFECTIVE RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2196 5 %RANDOM
Rwork0.239 ---
obs0.239 43932 62.9 %-
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.3 Å20 Å20 Å2
2---2.84 Å20 Å2
3---12.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19222 0 180 0 19402
Refine LS restraints
Refine-IDTypeDev ideal
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_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.55
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 350 5 %
Rwork0.295 6655 -
obs--61 %
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_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.55

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