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- PDB-1l2q: Crystal Structure of the Methanosarcina barkeri Monomethylamine M... -

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Basic information

Entry
Database: PDB / ID: 1l2q
TitleCrystal Structure of the Methanosarcina barkeri Monomethylamine Methyltransferase (MtmB)
Componentsmonomethylamine methyltransferase
KeywordsTRANSFERASE / Tim barrel
Function / homology
Function and homology information


methylamine-corrinoid protein Co-methyltransferase / monomethylamine methyltransferase activity / methanogenesis / methylation
Similarity search - Function
Monomethylamine methyltransferase MtmB / Monomethylamine methyltransferase MtmB / Monomethylamine methyltransferase MtmB superfamily / Monomethylamine methyltransferase MtmB / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Monomethylamine methyltransferase MtmB1
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsHao, B. / Gong, W. / Ferguson, T.K. / James, C.M. / Krzycki, J.A. / Chan, M.K.
CitationJournal: Science / Year: 2002
Title: A new UAG-encoded residue in the structure of a methanogen methyltransferase.
Authors: Hao, B. / Gong, W. / Ferguson, T.K. / James, C.M. / Krzycki, J.A. / Chan, M.K.
History
DepositionFeb 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 13, 2014Group: Non-polymer description / Structure summary
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_poly_seq_scheme / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_seq_num / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE AUTHORS HAVE INDICATED THAT THE METHYL GROUP IN THE RESIDUE XPL202A(CONFORMER A) AND ...HETEROGEN THE AUTHORS HAVE INDICATED THAT THE METHYL GROUP IN THE RESIDUE XPL202A(CONFORMER A) AND PYL202A(CONFORMER B) COULD BE A METHYL (CH3), AMINE (NH2), OR HYDOXYL (OH) GROUP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: monomethylamine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3262
Polymers50,3081
Non-polymers181
Water9,602533
1
A: monomethylamine methyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)301,95812
Polymers301,8506
Non-polymers1086
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+3/21
crystal symmetry operation11_556-x+y,y,-z+3/21
crystal symmetry operation12_566x,x-y+1,-z+3/21
Buried area28830 Å2
ΔGint53 kcal/mol
Surface area73810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.070, 158.070, 135.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1193-

HOH

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Components

#1: Protein monomethylamine methyltransferase


Mass: 50308.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri (archaea) / References: UniProt: O30642
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.88 Å3/Da / Density % sol: 74.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M (NH4)2SO4, 0.1M NaCl, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlprotein1drop
2200 mM1dropNaCl
350 mMMOPS1droppH6.0
41.6 Mammonium sulfate1reservoir
50.1 M1reservoirNaCl
60.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2000
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 105886 / Num. obs: 105886 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 29.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.7 / Num. unique all: 105886 / Rsym value: 0.281 / % possible all: 94.8
Reflection
*PLUS
Num. measured all: 513202 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 94.6 % / Rmerge(I) obs: 0.281

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Processing

Software
NameVersionClassification
PHASESphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.7→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 483332.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.175 10172 10 %RANDOM
Rwork0.161 ---
all-105886 --
obs-105886 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 88.4432 Å2 / ksol: 0.413464 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.7 Å20 Å2
2--0.75 Å20 Å2
3----1.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3517 0 1 533 4051
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.215 1523 9.7 %
Rwork0.205 14190 -
obs-10209 87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CIS.PAR
X-RAY DIFFRACTION4X9.PAR
X-RAY DIFFRACTION5X7.PAR
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.16 / Rfactor Rfree: 0.174 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.176
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Rfactor Rfree: 0.215 / Rfactor Rwork: 0.205 / Rfactor obs: 0.205

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