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- PDB-1r18: Drosophila protein isoaspartyl methyltransferase with S-adenosyl-... -

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Basic information

Entry
Database: PDB / ID: 1r18
TitleDrosophila protein isoaspartyl methyltransferase with S-adenosyl-L-homocysteine
ComponentsProtein-L-isoaspartate(D-aspartate)-O-methyltransferase
KeywordsTRANSFERASE / methyltransferase / isomerization / protein repair / S-adenosyl homocysteine
Function / homology
Function and homology information


Protein repair / protein-L-isoaspartate(D-aspartate) O-methyltransferase / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / protein modification process / methylation / defense response to bacterium / cytosol / cytoplasm
Similarity search - Function
Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature. / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / 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 / Protein-L-isoaspartate(D-aspartate) O-methyltransferase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBennett, E.J. / Bjerregaard, J. / Knapp, J.E. / Chavous, D.A. / Friedman, A.M. / Royer Jr., W.E. / O'Connor, C.M.
Citation
Journal: Biochemistry / Year: 2003
Title: Catalytic implications from the Drosophila protein L-isoaspartyl methyltransferase structure and site-directed mutagenesis.
Authors: Bennett, E.J. / Bjerregaard, J. / Knapp, J.E. / Chavous, D.A. / Friedman, A.M. / Royer Jr., W.E. / O'Connor, C.M.
#1: Journal: Protein Sci. / Year: 2002
Title: Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6A resolution and modeling of an isoaspartyl-containing peptide at the active site
Authors: Smith, C.D. / Carson, M. / Friedman, A.M. / Skinner, M.M. / Delucas, L. / Chantalat, L. / Weise, L. / Shirasawa, T. / Chattopadhyay, D.
History
DepositionSep 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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_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-L-isoaspartate(D-aspartate)-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9822
Polymers24,5981
Non-polymers3841
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Protein-L-isoaspartate(D-aspartate)-O-methyltransferase
hetero molecules

A: Protein-L-isoaspartate(D-aspartate)-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9654
Polymers49,1962
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3630 Å2
ΔGint-26 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.070, 45.250, 61.240
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein-L-isoaspartate(D-aspartate)-O-methyltransferase / Protein-beta-aspartate methyltransferase / PIMT / Protein L-isoaspartyl/D-aspartyl ...Protein-beta-aspartate methyltransferase / PIMT / Protein L-isoaspartyl/D-aspartyl methyltransferase / L-isoaspartyl protein carboxyl methyltransferase


Mass: 24597.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PCMT / Plasmid: pGEX2-T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q27869, protein-L-isoaspartate(D-aspartate) O-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Tris, 35% v/v Ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
235 %ethanol1reservoir
3100 mMTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2002 / Details: osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 8636 / Num. obs: 8636 / % possible obs: 89 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.232 / Num. unique all: 761 / Rsym value: 0.232 / % possible all: 79.6
Reflection
*PLUS
% possible obs: 89 % / Num. measured all: 14628
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 79.6 % / Num. unique obs: 761 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human PIMT (pdb code 1I1N)

1i1n


Resolution: 2.2→20.97 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 477 5.5 %RANDOM
Rwork0.194 ---
all0.203 8636 --
obs0.194 8636 87.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.122 Å2 / ksol: 0.318386 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20.83 Å2
2--2.59 Å20 Å2
3----4.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→20.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 26 77 1799
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.257 35 5.9 %
Rwork0.229 557 -
obs--59.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3LIGANDHIC.PARAMLIGANDHIC.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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