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- PDB-1i1n: HUMAN PROTEIN L-ISOASPARTATE O-METHYLTRANSFERASE WITH S-ADENOSYL ... -

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Basic information

Entry
Database: PDB / ID: 1i1n
TitleHUMAN PROTEIN L-ISOASPARTATE O-METHYLTRANSFERASE WITH S-ADENOSYL HOMOCYSTEINE
ComponentsPROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
KeywordsTRANSFERASE / METHYLTRANSFERASE / S-ADENOSYL HOMOCYSTEINE / PROTEIN REPAIR
Function / homology
Function and homology information


protein-L-isoaspartate(D-aspartate) O-methyltransferase / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / Protein repair / protein repair / protein methylation / extracellular vesicle / cadherin binding / extracellular exosome / cytoplasm / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSmith, C.D. / Chattopadhyay, D. / Carson, M. / Friedman, A.M. / Skinner, M.M.
CitationJournal: Protein Sci. / Year: 2002
Title: Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A 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
DepositionFeb 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9222
Polymers24,5371
Non-polymers3841
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.105, 53.917, 48.814
Angle α, β, γ (deg.)90.00, 116.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE


Mass: 24537.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIMT_HUMAN / Organ: FETAL BRAIN / Plasmid: PET21C / Production host: Escherichia coli (E. coli)
References: UniProt: P22061, 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.: 279 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, sodium cacodylate, magnesium acetate, DTT, bis-Tris acetate, S-adenosyl homocysteine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
25 %PEG80001reservoir
415 mMmagnesium acetate1reservoir
52.6 mMAdoHcy1reservoir
3sodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 25, 1997 / Details: MSC MIRRORS
RadiationMonochromator: NICKEL FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 31332 / % possible obs: 86.8 % / Observed criterion σ(I): -3 / Redundancy: 3.47 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 28
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.16 % / Rmerge(I) obs: 0.205 / % possible all: 34.1
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Num. obs: 28488 / % possible obs: 95.7 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å / % possible obs: 87.1 % / Redundancy: 1.4 % / Num. unique obs: 2587 / Rmerge(I) obs: 0.124

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DL5.PDB

1dl5


Resolution: 1.5→14.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 944740.24 / Data cutoff high rms absF: 944740.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE SAH TOPOLOGY/PARAMETER FILES FOR CNS WERE CREATED BY COMBINING THE STANDARD MET AND ADE ENTRIES. THE DEFAULT CNS DNA-RNA_REP.PARAM FOR RNA/DNA WAS MODIFIED IN ...Details: BULK SOLVENT MODEL USED. THE SAH TOPOLOGY/PARAMETER FILES FOR CNS WERE CREATED BY COMBINING THE STANDARD MET AND ADE ENTRIES. THE DEFAULT CNS DNA-RNA_REP.PARAM FOR RNA/DNA WAS MODIFIED IN THE LATER STAGES OF REFINEMENT. THE RIBOSE RING DIHEDRAL FORCE CONSTANTS WERE SET TO 0.0 TO ALLOW THE RIBOSE RING PUCKER TO FIT THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1513 5 %RANDOM
Rwork0.183 ---
obs0.183 30470 84.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.88 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å20 Å20.73 Å2
2---3.24 Å20 Å2
3----0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.5→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 26 279 2010
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 118 4.9 %
Rwork0.304 2310 -
obs--40.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2RNA-BONDS-ETC.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4RNA-DIHE.PARAMION.TOP
X-RAY DIFFRACTION5SAH.PARAMSAH.TOPOL
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 15 Å / Num. reflection obs: 27830 / σ(F): 0 / Num. reflection Rfree: 1384 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.343 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.304

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