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- PDB-4o29: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE from Pyrobaculum aerop... -

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Basic information

Entry
Database: PDB / ID: 4o29
TitlePROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE from Pyrobaculum aerophilum in COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE
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-ADENOSYL-L-HOMOCYSTEINE / Protein-L-isoaspartate O-methyltransferase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsSawaya, M.R. / Yeates, T.O. / Griffith, S.C.
Citation
Journal: Thesis / Year: 2002
Title: Structure of L-isoaspartyl (D-aspartyl) Methyltransferase
Authors: Griffith, S.C.
#1: Journal: 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
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Sep 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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,6212
Polymers23,2371
Non-polymers3841
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.720, 35.670, 66.290
Angle α, β, γ (deg.)90.000, 100.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23236.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: IM2 / Gene: PAE0701, pcm, PIMT / Plasmid: pTrcHis2-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q8ZYN0, 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.: 2 / 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: 1.85 Å3/Da / Density % sol: 33.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 70% MPD, 0.1M HEPES pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 1999
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.9→65.22 Å / Num. all: 3881 / Num. obs: 3881 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 78.84 Å2 / Rmerge(I) obs: 0.171 / Net I/σ(I): 7.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.9-2.970.6511.79111026488.9
2.97-3.050.7682.241658257100
3.05-3.140.7032.49195129699.7
3.14-3.240.543.45168625499.6
3.24-3.350.4753.771578245100
3.35-3.460.3395.32160825299.2
3.46-3.590.2636.571568241100
3.59-3.740.2547.29144923399.1
3.74-3.910.1978.641314213100
3.91-4.10.1749.57134121799.5
4.1-4.320.14111177193100
4.32-4.580.11812.971200199100
4.58-4.90.10913.61106917698.3
4.9-5.290.11412.141015169100
5.29-5.790.10912.28993159100
5.79-6.480.13211.9185714198.6
6.48-7.480.09114.2979013198.5
7.48-9.160.06817.51620104100
9.16-12.960.05519.985108898.9
12.960.06313.342174994.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.509 / Cor.coef. Fo:Fc: 0.41
Highest resolutionLowest resolution
Translation3.8 Å15 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
EPMR2.5phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JG1

1jg1


Resolution: 2.9→65.22 Å / Cor.coef. Fo:Fc: 0.9056 / Cor.coef. Fo:Fc free: 0.8308 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 351 9.05 %RANDOM
Rwork0.2102 ---
all0.2149 3878 --
obs0.2149 3878 99.11 %-
Solvent computationBsol: 104.889 Å2
Displacement parametersBiso max: 136.16 Å2 / Biso mean: 64.6522 Å2 / Biso min: 35 Å2
Baniso -1Baniso -2Baniso -3
1--19.0392 Å20 Å2-5.7532 Å2
2--16.6706 Å20 Å2
3---2.3686 Å2
Refine analyzeLuzzati coordinate error obs: 0.443 Å
Refinement stepCycle: LAST / Resolution: 2.9→65.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 26 2 1635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.758
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2619 91 8.47 %
Rwork0.2462 984 -
all0.2475 1075 -
obs--99.11 %
Refinement TLS params.Method: refined / Origin x: 37.9205 Å / Origin y: 48.3813 Å / Origin z: 50.0303 Å
111213212223313233
T0.0153 Å20.036 Å2-0.0957 Å2--0.1255 Å20.0282 Å2---0.3414 Å2
L4.8588 °2-0.8163 °2-1.0688 °2-3.0838 °20.3945 °2--3.4923 °2
S0.038 Å °0.1325 Å °-0.0028 Å °0.0217 Å °-0.1328 Å °0.0265 Å °-0.0014 Å °0.0804 Å °0.0948 Å °
Refinement TLS groupSelection details: { A|* }
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3sah.par
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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