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- PDB-3mgg: Crystal Structure of Methyl Transferase from Methanosarcina mazei -

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Basic information

Entry
Database: PDB / ID: 3mgg
TitleCrystal Structure of Methyl Transferase from Methanosarcina mazei
ComponentsMethyltransferase
KeywordsTRANSFERASE / NYSGXRC / PSI-II / Protein structure Initiative / structural genomics / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
Helix Hairpins - #1580 / : / Methyltransferase domain / Methyltransferase domain / Helix Hairpins / Vaccinia Virus protein VP39 / Helix non-globular / Special / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...Helix Hairpins - #1580 / : / Methyltransferase domain / Methyltransferase domain / Helix Hairpins / Vaccinia Virus protein VP39 / Helix non-globular / Special / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsSyed Ibrahim, B. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Methyl Transferase from Methanosarcina mazei
Authors: Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase


Theoretical massNumber of molelcules
Total (without water)62,9262
Polymers62,9262
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-16 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.805, 56.019, 234.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methyltransferase


Mass: 31463.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: MM_1949 / Plasmid: BC - pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
References: UniProt: Q8PVL4, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate, 25% Peg 3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2010 / Details: Mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 44542 / Num. obs: 44542 / % possible obs: 84.1 % / Redundancy: 12.9 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.653 / Num. unique all: 3943 / % possible all: 75.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→45.54 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 87742.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2140 5.1 %RANDOM
Rwork0.214 ---
obs0.214 42306 79.9 %-
all-44542 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.0945 Å2 / ksol: 0.324767 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2--4.43 Å20 Å2
3----5.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.86→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 0 312 4238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.442.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.86→1.98 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 290 5 %
Rwork0.231 5487 -
obs-4250 66.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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