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- PDB-3m1v: Structural Insight into Methyl-Coenzyme M Reductase Chemistry usi... -

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Basic information

Entry
Database: PDB / ID: 3m1v
TitleStructural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues
Components(Methyl-coenzyme M reductase I subunit ...) x 3
KeywordsTRANSFERASE / Methyl-Coenzyme M Reductase / Metal-binding / Methanogenesis / Methylation / Nickel
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
ACETATE ION / 1-THIOETHANESULFONIC ACID / FACTOR 430 / DI(HYDROXYETHYL)ETHER / 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 / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsCedervall, P.E. / Dey, M. / Ragsdale, S.W. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2010
Title: Structural insight into methyl-coenzyme M reductase chemistry using coenzyme B analogues.
Authors: Cedervall, P.E. / Dey, M. / Pearson, A.R. / Ragsdale, S.W. / Wilmot, C.M.
History
DepositionMar 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 20, 2015Group: Non-polymer description
Revision 1.3Mar 29, 2017Group: Non-polymer description
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software

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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)276,34931
Polymers272,6466
Non-polymers3,70325
Water44,3532462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55430 Å2
ΔGint-292 kcal/mol
Surface area60410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.016, 118.260, 122.387
Angle α, β, γ (deg.)90.00, 91.84, 90.00
Int Tables number4
Space group name H-MP1211

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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


Mass: 60508.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
Strain: Marburg / DSM 2133
References: UniProt: P11558, coenzyme-B sulfoethylthiotransferase
#2: Protein Methyl-coenzyme M reductase I subunit beta / MCR I beta / Coenzyme-B sulfoethylthiotransferase beta


Mass: 47148.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
Strain: Marburg / DSM 2133
References: UniProt: P11560, coenzyme-B sulfoethylthiotransferase
#3: Protein Methyl-coenzyme M reductase I subunit gamma / MCR I gamma / Coenzyme-B sulfoethylthiotransferase gamma


Mass: 28666.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
Strain: Marburg / DSM 2133
References: UniProt: P11562, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 9 types, 2487 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / 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-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#12: Water ChemComp-HOH / water


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

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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: 43.47 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop
Details: PEG 400, magnesium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2007
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 407511 / Num. obs: 405349 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.226
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
BioCARS-developedGUIdata collection
REFMAC5.5.0072phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→20.15 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.924 / SU ML: 0.036 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16217 20362 5 %RANDOM
Rwork0.1347 ---
obs0.13609 384868 98.76 %-
all-410300 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.404 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.7 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19098 0 232 2462 21792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.02221015
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4681.97828642
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35752757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09324.9021020
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.468153531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.85215124
X-RAY DIFFRACTIONr_chiral_restr0.1960.23135
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02116382
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2751.512990
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92220923
X-RAY DIFFRACTIONr_scbond_it2.94238025
X-RAY DIFFRACTIONr_scangle_it4.6744.57614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 1319 -
Rwork0.219 25791 -
obs--89.83 %

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