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- PDB-4isc: Crystal structure of a putative Methyltransferase from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 4isc
TitleCrystal structure of a putative Methyltransferase from Pseudomonas syringae
ComponentsMethyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Methyltransferase
Function / homology
Function and homology information


oligosaccharide biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function
SAM-dependent methyltransferase, NodS-like / Nodulation protein S (NodS) / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Methyltransferase, putative
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.78 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative Methyltransferase from Pseudomonas syringae
Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJan 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8952
Polymers18,8171
Non-polymers781
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.460, 43.460, 181.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

#1: Protein Methyltransferase


Mass: 18817.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q880M1
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Na acetate, 0.1 M Bis Tris propane, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2012 / Details: MIRRORS
RadiationMonochromator: SI{111} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.71→42.26 Å / Num. all: 5263 / Num. obs: 5263 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24.3
Reflection shellResolution: 2.71→2.78 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 369 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.78→42.26 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.857 / SU B: 29.215 / SU ML: 0.289 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27744 214 4.6 %RANDOM
Rwork0.19016 ---
obs0.19439 4459 95.78 %-
all-4459 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.574 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.78→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 4 37 1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191283
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9531738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7475153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96921.9766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.13315204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6661517
X-RAY DIFFRACTIONr_chiral_restr0.1040.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021984
LS refinement shellResolution: 2.78→2.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 13 -
Rwork0.225 298 -
obs--89.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7753-0.1084-1.59821.8696-0.50533.73550.1258-0.04660.1636-0.1083-0.0887-0.4349-0.05470.7158-0.03710.0330.0122-0.00190.24390.02750.258721.11587.227976.1018
23.08660.3701-0.72663.56241.89895.19780.1249-0.0907-0.28080.0079-0.0670.14730.68520.1839-0.05780.16740.0371-0.00010.04940.01140.14439.7157-1.626979.3589
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 119
2X-RAY DIFFRACTION2A120 - 187

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