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- PDB-1kr5: Crystal structure of human L-isoaspartyl methyltransferase -

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Basic information

Entry
Database: PDB / ID: 1kr5
TitleCrystal structure of human L-isoaspartyl methyltransferase
ComponentsProtein-L-isoaspartate O-methyltransferase
KeywordsTRANSFERASE / Rossmann-fold doubly-wound-alpha-beta-alpha-sandwich
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRyttersgaard, C. / Griffith, S.C. / Sawaya, M.R. / MacLaren, D.C. / Clarke, S. / Yeates, T.O.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of human L-isoaspartyl methyltransferase.
Authors: Ryttersgaard, C. / Griffith, S.C. / Sawaya, M.R. / MacLaren, D.C. / Clarke, S. / Yeates, T.O.
History
DepositionJan 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)24,9222
Polymers24,5371
Non-polymers3841
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.007, 53.698, 49.003
Angle α, β, γ (deg.)90.00, 115.60, 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) / Plasmid: pDM2x / 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.: 64 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Magnesium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2 M11MgAc
20.1 Mcacodylate11pH6.5
320 %PEG800011

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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: Mar 8, 2001
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 12501 / Num. obs: 12501 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.256 / % possible all: 75
Reflection
*PLUS
Lowest resolution: 44.2 Å / Num. measured all: 47131
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JG1

1jg1


Resolution: 2.1→44.19 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 641174.09 / Data cutoff high rms absF: 641174.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 731 6.1 %RANDOM
Rwork0.221 ---
all0.224 12501 --
obs0.224 11959 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.452 Å2 / ksol: 0.368707 e/Å3
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å20 Å25.86 Å2
2---17.41 Å20 Å2
3---14.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.1→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 26 64 1737
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 97 6.8 %
Rwork0.318 1334 -
obs-1334 64.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SAH.PARSAH.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor obs: 0.318

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