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- PDB-3r3h: Crystal structure of O-methyltransferase from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 3r3h
TitleCrystal structure of O-methyltransferase from Legionella pneumophila
ComponentsO-methyltransferase, SAM-dependent
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / O-methyltransferase / 000563 / SAM dependent
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-methyltransferase, SAM-dependent
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsAgarwal, R. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of O-methyltransferase from Legionella pneumophila
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionMar 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-methyltransferase, SAM-dependent
B: O-methyltransferase, SAM-dependent


Theoretical massNumber of molelcules
Total (without water)55,6762
Polymers55,6762
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-30 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.254, 52.254, 659.278
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein O-methyltransferase, SAM-dependent


Mass: 27838.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2277 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL
References: UniProt: Q5ZT85, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Li2SO4, 0.1M Tris pH 8.5, 20% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2010 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 17267 / Num. obs: 17267 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 25.6 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / Num. unique all: 1649 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: None

Resolution: 2.65→45.25 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 25214.53 / 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
Rfree0.29 521 3.1 %RANDOM
Rwork0.265 ---
obs0.265 16953 98.6 %-
all-17267 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.9847 Å2 / ksol: 0.329089 e/Å3
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1-11.01 Å210.68 Å20 Å2
2--11.01 Å20 Å2
3----22.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.65→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 0 8 3452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.85
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.486 70 2.6 %
Rwork0.394 2572 -
obs-2572 97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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