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- PDB-4ine: Crystal structure of N-methyl transferase (PMT-2) from Caenorhabd... -

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Basic information

Entry
Database: PDB / ID: 4ine
TitleCrystal structure of N-methyl transferase (PMT-2) from Caenorhabditis elegant complexed with S-adenosyl homocysteine and phosphoethanolamine
ComponentsProtein PMT-2
KeywordsTRANSFERASE / methyl transferase
Function / homology
Function and homology information


phosphatidyl-N-methylethanolamine N-methyltransferase activity / phosphoethanolamine N-methyltransferase activity / phosphoethanolamine N-methyltransferase / N-methyltransferase activity / phosphatidylcholine biosynthetic process / methylation
Similarity search - Function
Phosphoethanolamine N-methyltransferase 2, N-terminal / Phosphoethanolamine N-methyltransferase 2 N-terminal / Methyltransferase type 11 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / S-ADENOSYL-L-HOMOCYSTEINE / Phosphoethanolamine N-methyltransferase 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLukk, T. / Nair, S.K.
CitationJournal: To be Published
Title: Crystal structure of N-methyl transferase (PMT-2) from Caenorhabditis elegant complexed with S-adenosyl homocysteine and phosphoethanolamine
Authors: Lukk, T. / Nair, S.K.
History
DepositionJan 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Protein PMT-2
B: Protein PMT-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6298
Polymers103,4222
Non-polymers1,2076
Water19,5641086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-8 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.131, 68.011, 74.742
Angle α, β, γ (deg.)107.18, 96.30, 106.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein PMT-2


Mass: 51710.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pmt-2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q22993
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID


Mass: 141.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8NO4P
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SPECIFIC CLONE IS AN ISOFORM OF THE SEQUENCE OF UNP ENTRY Q22993. RESIDUES LYS 89 AND ASN 93 ...THE SPECIFIC CLONE IS AN ISOFORM OF THE SEQUENCE OF UNP ENTRY Q22993. RESIDUES LYS 89 AND ASN 93 ARE LINKED TOGETHER

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution was at 15 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME, 5 mM SAH, 5 mM phosphoethanolamine. Mother liqueur contained 0.04 M potassium ...Details: Protein solution was at 15 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME, 5 mM SAH, 5 mM phosphoethanolamine. Mother liqueur contained 0.04 M potassium phosphate (monobasic), 16% PEG 8,000 and 20% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 3, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 172409 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.05 / Net I/σ(I): 11.6
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.634 / % possible all: 93.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3UJB

3ujb


Resolution: 1.45→29.63 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 1.059 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0713 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.194 7671 5 %RANDOM
Rwork0.17 ---
obs0.172 152982 85.7 %-
all-178550 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20.01 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6914 0 76 1086 8076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.027239
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9529802
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60224.578367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.391151242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4551540
X-RAY DIFFRACTIONr_chiral_restr0.0880.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 186 -
Rwork0.221 3471 -
obs--27.81 %

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