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- PDB-1e2l: Kinetics and crystal structure of the wild-type and the engineere... -

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Basic information

Entry
Database: PDB / ID: 1e2l
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
KeywordsTHYMIDINE 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 18, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2236
Polymers71,5262
Non-polymers6974
Water2,702150
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, 118.300, 108.600
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: (-0.91739, -0.34284, -0.20215), (-0.33735, 0.40034, 0.85201), (-0.21117, 0.84982, -0.48292)
Vector: 75.40794, 24.21157, -9.7035)
DetailsTHE STRONG CRYSTAL PACKING GENERATED USING X , 1-Y, -Z GIVESCHAIN A TO CHAIN A (SYMMETRY RELATED) CONTACTS.

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Components

#1: Protein THYMIDINE KINASE


Mass: 35763.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
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.: 150 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A AND B ENGINEERED MUTATION TYR101PHE

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growpH: 7.5 / Details: LITHIUM SULFATE, HEPES, DTT, (N)-MCT, 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU/MSC FR-C / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1999
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 27908 / % possible obs: 97 % / Redundancy: 3.4 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.5 / % possible all: 96
Reflection shell
*PLUS
Rmerge(I) obs: 0.5

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Processing

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

1vtk


Resolution: 2.4→20 Å / SU B: 4.5 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.27
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1396 5 %RANDOM
Rwork0.21 ---
obs-27908 97 %-
Displacement parametersBiso mean: 38.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 46 150 4880
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
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: 0.211 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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