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- PDB-1nth: Crystal structure of the methanosarcina barkeri monomethylamine m... -

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Basic information

Entry
Database: PDB / ID: 1nth
TitleCrystal structure of the methanosarcina barkeri monomethylamine methyltransferase (MTMB)
ComponentsMonomethylamine methyltransferase mtmB1
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
Monomethylamine methyltransferase MtmB1
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.55 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
DepositionJan 30, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 4, 2003ID: 1L2R
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN THE AUTHORS HAVE INDICATED THAT THE METHYL GROUP IN THE RESIDUE PYL202A COULD BE A METHYL ...HETEROGEN THE AUTHORS HAVE INDICATED THAT THE METHYL GROUP IN THE RESIDUE PYL202A 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 mtmB1


Theoretical massNumber of molelcules
Total (without water)50,2911
Polymers50,2911
Non-polymers00
Water8,341463
1
A: Monomethylamine methyltransferase mtmB1
x 6


Theoretical massNumber of molelcules
Total (without water)301,7476
Polymers301,7476
Non-polymers00
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 area25470 Å2
ΔGint-7 kcal/mol
Surface area74300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.464, 158.464, 135.797
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-880-

HOH

DetailsThe biological assembly is a hexamer

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Components

#1: Protein Monomethylamine methyltransferase mtmB1 / MMA methyltransferase 1 / MMAMT 1


Mass: 50291.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri (archaea) / Strain: MS
References: UniProt: O30642, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 4.29 Å3/Da / Density % sol: 71.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4.3M NACL, 0.1M HEPES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Jun 1, 2001 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. all: 140499 / Num. obs: 140499 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 16.8
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / Num. unique all: 13348 / Rsym value: 0.51 / % possible all: 93.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.55→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.188 13401 -RANDOM
Rwork0.176 ---
all-140499 --
obs-140499 97.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.732 Å2-0.732 Å2-0.863 Å2
2--0 Å20 Å2
3---1.465 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 0 463 3962
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it0.9161.5
X-RAY DIFFRACTIONc_mcangle_it1.3112
X-RAY DIFFRACTIONc_scbond_it1.7892
X-RAY DIFFRACTIONc_scangle_it2.7022.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.007
RfactorNum. reflection% reflection
Rfree0.293 1934 -
Rwork0.29 --
obs-17472 81.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3cis.param
X-RAY DIFFRACTION4x8b.param
X-RAY DIFFRACTION5bg6b.param

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