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- PDB-3pot: Structural analysis of a Ni(III)-methyl species in methyl-coenzym... -

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Entry
Database: PDB / ID: 3pot
TitleStructural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis
Components(Methyl-coenzyme M reductase I subunit ...) x 3
KeywordsTRANSFERASE / METAL-BINDING / NICKEL / METHYL-COENZYME M REDUCTASE / 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
Iodomethane / 1-THIOETHANESULFONIC ACID / FACTOR 430 / : / Coenzyme B / O-phosphono-N-(6-sulfanylhexanoyl)-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: 1.2 Å
AuthorsCedervall, P.E. / Wilmot, C.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structural Analysis of a Ni-Methyl Species in Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis.
Authors: Cedervall, P.E. / Dey, M. / Li, X. / Sarangi, R. / Hedman, B. / Ragsdale, S.W. / Wilmot, C.M.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: 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 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_alt_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.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_alt_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.value / _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.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_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)277,55330
Polymers273,4336
Non-polymers4,12024
Water46,8752602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53930 Å2
ΔGint-290 kcal/mol
Surface area60140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.886, 118.165, 122.388
Angle α, β, γ (deg.)90.00, 91.94, 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: 60639.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P11558, coenzyme-B sulfoethylthiotransferase
#2: Protein Methyl-coenzyme M reductase I subunit beta / MCR I beta / Coenzyme-B sulfoethylthiotransferase beta


Mass: 47279.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P11560, coenzyme-B sulfoethylthiotransferase
#3: Protein Methyl-coenzyme M reductase I subunit gamma / MCR I gamma / Coenzyme-B sulfoethylthiotransferase gamma


Mass: 28797.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P11562, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 9 types, 2626 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / 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-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#7: Chemical ChemComp-TXZ / O-phosphono-N-(6-sulfanylhexanoyl)-L-threonine


Mass: 329.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20NO7PS
#8: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO7PS
#9: Chemical ChemComp-06C / Iodomethane / Methyl iodine


Mass: 141.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3I
#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2602 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details06C HAS REACTED WITH THE ENZYME METAL CENTER TO YIELD A NI-BOUND METHYL GROUP (CH3) (THE NI IS PART ...06C HAS REACTED WITH THE ENZYME METAL CENTER TO YIELD A NI-BOUND METHYL GROUP (CH3) (THE NI IS PART OF COFACTOR F430) AND AN IODIDE (I-) THAT IS SITUATED IN THE ACTIVE SITE AT A DISTANCE OF 4 ANGSTROM FROM CH3

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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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Hepes-Na pH 7.5, 150 mM magnesium acetate and 20% PEG 400., VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2009
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 721334 / Num. obs: 721334 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 13.27 Å2 / Rsym value: 0.075 / Net I/σ(I): 19.5
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 72029 / Rsym value: 0.43 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ID: 3M2R, but with all waters, coenzymes and metal ions removed
Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.05 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1562 36128 5 %RANDOM
Rwork0.13173 ---
obs0.13295 685122 99.9 %-
all-685808 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.192 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0.15 Å2
2--0.39 Å2-0 Å2
3----0.37 Å2
Refine analyzeLuzzati coordinate error obs: 0.1779 Å
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19098 0 241 2602 21941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02220078
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.931.97627256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29552542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54424.713957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.331153296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.92615119
X-RAY DIFFRACTIONr_chiral_restr0.1280.22991
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02115503
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_it1.0881.512457
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.761219966
X-RAY DIFFRACTIONr_scbond_it2.67737621
X-RAY DIFFRACTIONr_scangle_it4.2954.57253
X-RAY DIFFRACTIONr_rigid_bond_restr1.565320078
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 2697 -
Rwork0.194 50103 -
obs-50103 99.06 %

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