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- PDB-1tv2: Crystal structure of the hydroxylamine MtmB complex -

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Basic information

Entry
Database: PDB / ID: 1tv2
TitleCrystal structure of the hydroxylamine MtmB complex
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
Chem-BG5 / Monomethylamine methyltransferase MtmB1
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHao, B. / Zhao, G. / Kang, P.T. / Soares, J.A. / Ferguson, T.K. / Gallucci, J. / Krzycki, J.A. / Chan, M.K.
CitationJournal: Chem.Biol. / Year: 2004
Title: Reactivity and chemical synthesis of L-pyrrolysine- the 22(nd) genetically encoded amino acid
Authors: Hao, B. / Zhao, G. / Kang, P.T. / Soares, J.A. / Ferguson, T.K. / Gallucci, J. / Krzycki, J.A. / Chan, M.K.
History
DepositionJun 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Monomethylamine methyltransferase mtmB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3432
Polymers50,1831
Non-polymers1601
Water8,305461
1
A: Monomethylamine methyltransferase mtmB1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)302,06012
Polymers301,0996
Non-polymers9616
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 area25740 Å2
ΔGint-4 kcal/mol
Surface area73700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.170, 158.170, 136.210
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-849-

HOH

21A-850-

HOH

31A-853-

HOH

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Components

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


Mass: 50183.117 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: Chemical ChemComp-BG5 / 5-HYDROXYAMINO-3-METHYL-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 160.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 71.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NACL, HEPES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.992 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 11, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 67189 / Num. obs: 67189 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.177 / Rsym value: 0.177 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3307 / Rsym value: 0.593 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1NTH

1nth


Resolution: 2→19.97 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 311870.26 / 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
Rfree0.183 6380 10.1 %RANDOM
Rwork0.165 ---
all0.165 62969 --
obs0.165 62969 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.3925 Å2 / ksol: 0.395048 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å22.69 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 10 461 3962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 943 9.7 %
Rwork0.226 8779 -
obs-9650 87.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3BG5NO.PARAM
X-RAY DIFFRACTION4CIS.PARAM

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