[English] 日本語
Yorodumi
- PDB-1jms: Crystal Structure of the Catalytic Core of Murine Terminal Deoxyn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jms
TitleCrystal Structure of the Catalytic Core of Murine Terminal Deoxynucleotidyl Transferase
ComponentsTERMINAL DEOXYNUCLEOTIDYLTRANSFERASE
KeywordsTRANSFERASE / polymerase / nucleotidyl transferase
Function / homology
Function and homology information


DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / DNA-directed DNA polymerase activity / hydrolase activity ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / DNA-directed DNA polymerase activity / hydrolase activity / DNA repair / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA nucleotidylexotransferase (TdT) / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda ...DNA nucleotidylexotransferase (TdT) / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / breast cancer carboxy-terminal domain / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA nucleotidylexotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.36 Å
AuthorsDelarue, M. / Boule, J.B. / Lescar, J. / Expert-Bezancon, N. / Sukumar, N. / Jourdan, N. / Rougeon, F. / Papanicolaou, C.
Citation
Journal: Embo J. / Year: 2002
Title: Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.
Authors: Delarue, M. / Boule, J.B. / Lescar, J. / Expert-Bezancon, N. / Jourdan, N. / Sukumar, N. / Rougeon, F. / Papanicolaou, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization of the Catalytic Domain of Murine Deoxynucleotidyl Transferase
Authors: Sukumar, N. / Boule, J.B. / Expert-Bezancon, N. / Jourdan, N. / Lescar, J. / Rougeon, F. / Papanicolaou, C. / Delarue, M.
History
DepositionJul 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6503
Polymers43,6031
Non-polymers472
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.100, 85.200, 111.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE / TERMINAL ADDITION ENZYME


Mass: 43602.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: short isoform / Source: (gene. exp.) Mus musculus (house mouse) / Gene: TDT / Plasmid: pET28(b) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P09838, DNA nucleotidylexotransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, LiCl 1M, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 253 K
Details: Sukumar, N., (2000) Acta Crystallogr., Sect.D, 56, 1662.
pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH6.8
2200 mM1dropNaCl
350 mM1dropMg(OAc)2
4100 mMammonium sulfate1drop
510 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.94 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 25, 1999
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. all: 19351 / Num. obs: 19351 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 25.3
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.34 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 99454
Reflection shell
*PLUS
% possible obs: 98.4 % / Num. unique obs: 1224 / Rmerge(I) obs: 0.34

-
Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.36→18 Å / Data cutoff high rms absF: 1000 / Isotropic thermal model: yes / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.259 968 5 %random
Rwork0.214 ---
all0.218 18766 --
obs0.218 18766 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.91 Å2 / ksol: 0.3511 e/Å3
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.696 Å20 Å20 Å2
2--6.953 Å20 Å2
3----14.649 Å2
Refinement stepCycle: LAST / Resolution: 2.36→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 2 214 3125
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.092
X-RAY DIFFRACTIONc_mcbond_it1.4331.5
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_mcangle_it2.3552
X-RAY DIFFRACTIONc_scangle_it3.4142.5
LS refinement shellResolution: 2.36→2.4 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.38 45 5 %
Rwork0.3178 841 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 18 Å / Num. reflection obs: 17984 / σ(F): 0 / Num. reflection Rfree: 973 / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_angle_deg1.08
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.38 / % reflection Rfree: 5 %

+
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