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- PDB-6mro: Crystal structure of methyl transferase from Methanosarcina aceti... -

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Basic information

Entry
Database: PDB / ID: 6mro
TitleCrystal structure of methyl transferase from Methanosarcina acetivorans at 1.6 Angstroms resolution, Northeast Structural Genomics Consortium (NESG) Target MvR53.
Componentsmethyl transferase from Methanosarcina acetivoransMethyltransferase
KeywordsTRANSFERASE / methyl transferase / SAH / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function
TPMT family / Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile. / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransf_25 domain-containing protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSingh, S. / Forouhar, F. / Wang, C. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To Be Published
Title: Crystal structure of a methyl transferase from Methanosarcina acetivorans at 1.6 Angstroms resolution.
Authors: Singh, S. / Forouhar, F. / Wang, C. / Vorobiev, S.M. / Neky, M.J. / Hunt, J.F.
History
DepositionOct 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: methyl transferase from Methanosarcina acetivorans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,74012
Polymers21,9921
Non-polymers74811
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.990, 40.990, 104.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein methyl transferase from Methanosarcina acetivorans / Methyltransferase


Mass: 21992.178 Da / Num. of mol.: 1 / Mutation: D65R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) (archaea)
Strain: ATCC 35395 / DSM 2834 / JCM 12185 / C2A / Gene: MA_2137 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TNZ0
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 7
Details: 0.2M Calcium chloride dihydrate 0.1M MES 6.0 20% w/v PEG-6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40.99 Å / Num. obs: 22761 / % possible obs: 99.59 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09546 / Rpim(I) all: 0.03797 / Net I/σ(I): 12.54
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.458 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 2267 / CC1/2: 0.493 / Rpim(I) all: 0.6174 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NEC
Resolution: 1.6→40.99 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.05
RfactorNum. reflection% reflection
Rfree0.21 2251 5.02 %
Rwork0.1793 --
obs0.1809 22761 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 10 149 1733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061737
X-RAY DIFFRACTIONf_angle_d0.9492365
X-RAY DIFFRACTIONf_dihedral_angle_d12.2131408
X-RAY DIFFRACTIONf_chiral_restr0.06252
X-RAY DIFFRACTIONf_plane_restr0.007315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.63490.35131320.34572664X-RAY DIFFRACTION99
1.6349-1.6730.36271370.31712599X-RAY DIFFRACTION99
1.673-1.71480.30141450.30222694X-RAY DIFFRACTION100
1.7148-1.76120.32351450.28662704X-RAY DIFFRACTION100
1.7612-1.8130.27051410.26082646X-RAY DIFFRACTION100
1.813-1.87150.28611450.24072695X-RAY DIFFRACTION100
1.8715-1.93840.26571340.22042646X-RAY DIFFRACTION100
1.9384-2.0160.24951440.19052637X-RAY DIFFRACTION100
2.016-2.10780.21481450.1872652X-RAY DIFFRACTION100
2.1078-2.21890.23471450.17152660X-RAY DIFFRACTION100
2.2189-2.35790.20811470.17122643X-RAY DIFFRACTION100
2.3579-2.53990.17461320.17682694X-RAY DIFFRACTION100
2.5399-2.79550.18111370.1712646X-RAY DIFFRACTION99
2.7955-3.19980.18741400.16232680X-RAY DIFFRACTION99
3.1998-4.03090.18211410.13932660X-RAY DIFFRACTION100
4.0309-41.00340.1791410.14742661X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.8004 Å / Origin y: -5.213 Å / Origin z: -0.9919 Å
111213212223313233
T0.145 Å20.0115 Å2-0.0058 Å2-0.1665 Å20.0062 Å2--0.2477 Å2
L1.9722 °20.0308 °20.5036 °2-2.2959 °2-0.9459 °2--1.8627 °2
S-0.0892 Å °-0.197 Å °0.1353 Å °0.0124 Å °0.0242 Å °0.1002 Å °-0.0089 Å °-0.0809 Å °0.0419 Å °
Refinement TLS groupSelection details: all

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