[English] 日本語
Yorodumi
- PDB-1e2k: Kinetics and crystal structure of the wild-type and the engineere... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e2k
TitleKinetics and crystal structure of the wild-type and the engineered Y101F mutant of Herpes simplex virus type 1 thymidine kinase interacting with (North)-methanocarba-thymidine
ComponentsTHYMIDINE KINASE
KeywordsTRANSFERASE / THYMIDINE KINASE / ANTIVIRAL DRUG / ENZYME-PRODRUG GENE THERAPY / SUGAR RING PUCKER
Function / homology
Function and homology information


TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / ATP binding
Similarity search - Function
Herpesvirus thymidine kinase / Thymidine kinase from herpesvirus / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TMC / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHERPES SIMPLEX VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVogt, J. / Scapozza, L. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 2000
Title: Kinetics and Crystal Structure of the Wild-Type and the Engineered Y101F Mutant of Herpes Simplex Virus Type 1 Thymidine Kinase Interacting with (North)-Methanocarba-Thymidine
Authors: Prota, A. / Vogt, J. / Pilger, B. / Perozzo, R. / Wurth, C. / Marquez, V. / Russ, P. / Schulz, G.E. / Folkers, G. / Scapozza, L.
#1: Journal: FEBS Lett. / Year: 1995
Title: The Three-Dimensional Structure of Thymidine Kinase from Herpes Simplex Virus Type 1
Authors: Wild, K. / Bohner, T. / Aubry, A. / Folkers, G. / Schulz, G.E.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: Crystal Structures of the Thymidine Kinase from Herpes Simplex Virus Type-1 in Complex with Deoxythymidine and Ganciclovir
Authors: Brown, D.G. / Visse, R. / Sandhu, G. / Davies, A. / Rizkallah, P.J. / Melitz, C. / Summers, W.C. / Sanderson, M.R.
History
DepositionMay 23, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2556
Polymers71,5582
Non-polymers6974
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.000, 117.700, 108.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92536, -0.3241, -0.19663), (-0.32539, 0.41298, 0.85063), (-0.19448, 0.85112, -0.48761)
Vector: 74.95271, 23.26896, -10.05367)
DetailsTHE STRONG CRYSTAL PACKING GENERATED USING X , 1-Y, -Z GIVESCHAIN A TO CHAIN A (SYMMETRY RELATED) CONTACTS.

-
Components

#1: Protein THYMIDINE KINASE


Mass: 35779.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HERPES SIMPLEX VIRUS (TYPE 1/ STRAIN 17)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TMC / 1-[4-HYDROXY-5-(HYDROXYMETHYL)BICYCLO[3.1.0]HEX-2-YL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE / (N)-METHANOCARBA-THYMIDINE


Mass: 252.266 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growpH: 7.5 / Details: LITHIUM SULFATE, HEPES, DTT, pH 7.50
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
20.9-1.2 M1reservoirLi2SO4
31 mMdithiothreitol1reservoir
40.1 MHEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8468
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8468 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 79549 / % possible obs: 99 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.58 / % possible all: 99
Reflection
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.05

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VTK

1vtk


Resolution: 1.7→20 Å / SU B: 1.3 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3978 5 %RANDOM
Rwork0.209 ---
obs-79549 99 %-
Displacement parametersBiso mean: 32.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4759 0 46 364 5169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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