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- PDB-3m30: Structural Insight into Methyl-Coenzyme M Reductase Chemistry usi... -

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Basic information

Entry
Database: PDB / ID: 3m30
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 / Nickel / Metal-binding / Methanogenesis / Methylation
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 / O-phosphono-N-(9-sulfanylnonanoyl)-L-threonine / 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 8, 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)277,05433
Polymers272,6466
Non-polymers4,40827
Water42,6602368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55090 Å2
ΔGint-280 kcal/mol
Surface area60200 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 , 10 types, 2395 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-XP9 / O-phosphono-N-(9-sulfanylnonanoyl)-L-threonine


Mass: 371.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26NO7PS
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#12: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2368 / 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: 409587 / Num. obs: 401701 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.283
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.167 / % possible all: 95.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
BioCARS-developedGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0072phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→20.07 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.948 / SU ML: 0.036 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16438 20163 5 %RANDOM
Rwork0.13583 ---
obs0.13727 381474 97.08 %-
all-413737 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.931 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.09 Å2
2--0.66 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19098 0 275 2368 21741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.02220858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5491.98128415
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37452714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46624.9361015
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42153470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.96915123
X-RAY DIFFRACTIONr_chiral_restr0.1970.23101
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02116257
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_it1.2761.512866
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.909220730
X-RAY DIFFRACTIONr_scbond_it2.94937992
X-RAY DIFFRACTIONr_scangle_it4.714.57591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.484 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 1210 -
Rwork0.219 23611 -
obs--81.48 %

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