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- PDB-1dl5: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1dl5
TitlePROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
ComponentsPROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
KeywordsTRANSFERASE / METHYLTRANSFERASE / ISOASPARTYL RESIDUES / PROTEIN REPAIR / DEAMIDATION / POST-TRANSLATIONAL MODIFICATION
Function / homology
Function and homology information


protein-L-isoaspartate(D-aspartate) O-methyltransferase / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / protein repair / cytoplasm
Similarity search - Function
Protein-l-isoaspartate O-methyltransferase; Chain: A, domain 2 / Protein-L-isoaspartyl O-methyltransferase, C-terminal domain / Protein-L-isoaspartyl O-methyltransferase, C-terminal / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature. / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / 3-Layer(bab) Sandwich / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...Protein-l-isoaspartate O-methyltransferase; Chain: A, domain 2 / Protein-L-isoaspartyl O-methyltransferase, C-terminal domain / Protein-L-isoaspartyl O-methyltransferase, C-terminal / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature. / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / 3-Layer(bab) Sandwich / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsSkinner, M.M. / Puvathingal, J.M. / Walter, R.L. / Friedman, A.M.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair.
Authors: Skinner, M.M. / Puvathingal, J.M. / Walter, R.L. / Friedman, A.M.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,01723
Polymers72,8822
Non-polymers2,13521
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-153 kcal/mol
Surface area26600 Å2
MethodPISA
2
B: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)75,01723
Polymers72,8822
Non-polymers2,13521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3800 Å2
ΔGint-162 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.060, 98.910, 76.860
Angle α, β, γ (deg.)90.0, 105.66, 90.0
Int Tables number4
Space group name H-MP1211
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT IS A DIMER (CHAIN A AND B) RELATED BY THE NON-CRYSTALLOGRAPHIC SYMMETRY OPERATOR. FUNCTIONAL OLIGOMERIZATION STATE IS UNKNOWN.

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Components

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


Mass: 36440.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET30B / Production host: Escherichia coli (E. coli)
References: UniProt: Q56308, protein-L-isoaspartate(D-aspartate) O-methyltransferase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd / Details: COMMERCIAL SOURCE (SIGMA )
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.57 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: THREE MICROLITERS OF PROTEIN AT A CONCENTRATION OF 6.3MGS/ML IN 10MM TRIS PH 8.0, 200MM NACL, 5% GLYCEROL, LMM DTT, 5MM BME AND 0.1MM EDTA WERE MIXED WITH THREE MICROLITERS OF A RESERVOIR ...Details: THREE MICROLITERS OF PROTEIN AT A CONCENTRATION OF 6.3MGS/ML IN 10MM TRIS PH 8.0, 200MM NACL, 5% GLYCEROL, LMM DTT, 5MM BME AND 0.1MM EDTA WERE MIXED WITH THREE MICROLITERS OF A RESERVOIR SOLUTION OF 28% PEG400, 100MM SODIUM ACETATE PH 4.5, AND 100MM CADMIUM CHLORIDE AND EQUILIBRATED AGAINST THE SAME., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
128 %(v/v)PEG4001reservoir
2100 mM1reservoirNaOAc
3100 mM 1reservoirCdCl2or ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 11, 1999 / Details: MSC/YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. all: 67929 / Num. obs: 66308 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 10 / % possible all: 95.7
Reflection
*PLUS
Highest resolution: 1.65 Å
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 1.8→15 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: TORSIONAL DYNAMICS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 4051 6 %SHELLS
Rwork0.182 ---
obs0.182 66212 97.5 %-
all-67917 --
Displacement parametersBiso mean: 22.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.265 Å20 Å23.536 Å2
2---0.776 Å20 Å2
3---0.168 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5106 0 71 463 5640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.376
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.88
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.787
X-RAY DIFFRACTIONc_mcangle_it2.393
X-RAY DIFFRACTIONc_scbond_it2.892
X-RAY DIFFRACTIONc_scangle_it4.102
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.255 337 6 %
Rwork0.207 5028 -
obs--95.7 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 66308
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.88
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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