[English] 日本語
Yorodumi
- PDB-1dl5: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE -

+
Open data


ID or keywords:

Loading...

-
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 / protein modification process / methylation / 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-isoaspartyl O-methyltransferase, C-terminal domain / Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature. / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / 3-Layer(bab) Sandwich / Vaccinia Virus protein VP39 ...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-isoaspartyl O-methyltransferase, C-terminal domain / Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature. / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / 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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more