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- PDB-1jg3: Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 1jg3
TitleCrystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrate
Components
  • VYP(L-iso-ASP)HA
  • protein-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
ADENOSINE / Protein-L-isoaspartate O-methyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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
B: protein-L-isoaspartate O-methyltransferase
C: VYP(L-iso-ASP)HA
D: VYP(L-iso-ASP)HA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,28110
Polymers54,6304
Non-polymers6516
Water3,783210
1
A: protein-L-isoaspartate O-methyltransferase
C: VYP(L-iso-ASP)HA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6415
Polymers27,3152
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-23 kcal/mol
Surface area9690 Å2
MethodPISA
2
B: protein-L-isoaspartate O-methyltransferase
D: VYP(L-iso-ASP)HA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6415
Polymers27,3152
Non-polymers3263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-24 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.573, 91.573, 124.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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.: 2
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: Protein/peptide VYP(L-iso-ASP)HA


Mass: 701.747 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: hexapeptide substrate

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Non-polymers , 4 types, 216 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50% MPD, 100mM Tris-HCl, 200mM ammonium phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
20.5 M1dropNaCl
320 mMHEPES1drop
450 %(v/v)MPD1reservoir
5100 mMTris-HCl1reservoir
6200 mMammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2001
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→500 Å / Num. all: 39722 / Num. obs: 39722 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.106 / Rsym value: 0.106
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.435 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 500 Å / Num. measured all: 235211
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1986 5 %random
Rwork0.204 ---
obs0.211 39722 --
all-39722 --
Refinement stepCycle: LAST / Resolution: 2.1→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 42 210 3746
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
Refinement
*PLUS
Lowest resolution: 500 Å / σ(F): 0 / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS

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