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- PDB-1jg4: Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 1jg4
TitleCrystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with S-adenosylmethionine
Componentsprotein-L-isoaspartate O-methyltransferase
KeywordsTRANSFERASE / Rossmann methyltransferase / PROTEIN REPAIR ISOMERIZATION
Function / homology
Function and homology information


protein-L-isoaspartate(D-aspartate) O-methyltransferase / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / protein repair / protein modification process / methylation / 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-ADENOSYLMETHIONINE / Protein-L-isoaspartate O-methyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGriffith, S.C. / Sawaya, M.R. / Boutz, D. / Thapar, N. / Katz, J. / Clarke, S. / Yeates, T.O.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate.
Authors: Griffith, S.C. / Sawaya, M.R. / Boutz, D.R. / Thapar, N. / Katz, J.E. / Clarke, S. / Yeates, T.O.
History
DepositionJun 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: protein-L-isoaspartate O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0122
Polymers26,6131
Non-polymers3981
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.502, 52.701, 97.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein protein-L-isoaspartate O-methyltransferase / E.C.2.1.1.77 / PROTEIN-BETA-ASPARTATE METHYLTRANSFERASE / PIMT / PROTEIN L-ISOASPARTYL METHYLTRANSFERASE / L- ...PROTEIN-BETA-ASPARTATE METHYLTRANSFERASE / PIMT / PROTEIN L-ISOASPARTYL METHYLTRANSFERASE / L-ISOASPARTYL PROTEIN CARBOXYL METHYLTRANSFERASE


Mass: 26613.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TZR3, protein-L-isoaspartate(D-aspartate) O-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.91 Å3/Da / Density % sol: 35.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG 2000, 15% Glycerol, 0.2 M Ammonium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
20.5 M1dropNaCl
320 mMHEPES1drop
425 %(w/v)PEG20001reservoir
515 %(v/v)glycerol1reservoir
60.2 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2000
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→500 Å / Num. all: 33412 / Num. obs: 33412 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.041 / Rsym value: 0.041
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.331 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 500 Å / Num. measured all: 234242
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 6.6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1671 5 %random
Rwork0.206 ---
all-33412 --
obs-33412 --
Refinement stepCycle: LAST / Resolution: 1.5→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 27 177 1901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

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