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- PDB-8y7w: Thymidine Kinase from Staphylococcus aureus(COL strain) -

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Basic information

Entry
Database: PDB / ID: 8y7w
TitleThymidine Kinase from Staphylococcus aureus(COL strain)
ComponentsThymidine kinase
KeywordsTRANSFERASE / Native
Function / homology
Function and homology information


thymidine metabolic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAshraf, A. / Pal, R.K. / Hassan, M.I.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchNo.R.1201/06/2022-HR/E India
CitationJournal: To Be Published
Title: Thymidine Kinase from Staphylococcus aureus(COL strain)
Authors: Ashraf, A. / Pal, R.K. / Hassan, M.I.
History
DepositionFeb 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3075
Polymers23,0741
Non-polymers2324
Water1,15364
1
A: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,22720
Polymers92,2974
Non-polymers93016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area9440 Å2
ΔGint-192 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.736, 71.736, 95.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-451-

HOH

31A-456-

HOH

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Components

#1: Protein Thymidine kinase


Mass: 23074.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Gene: tdk, SACOL2111 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HE81, thymidine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 1.6M Ammonium Sulfate 0.1M MES 10% V/V 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 11525 / % possible obs: 99.6 % / Redundancy: 21.9 % / CC1/2: 0.992 / Net I/σ(I): 35.52
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1126 / CC1/2: 0.983

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.14 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.939 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22735 560 4.9 %RANDOM
Rwork0.19258 ---
obs0.19436 10875 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-0 Å20 Å2
2--0.98 Å2-0 Å2
3----1.97 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1349 0 8 64 1421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131383
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151325
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.6331872
X-RAY DIFFRACTIONr_angle_other_deg1.51.5813058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2995181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45322.0967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97715242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4861510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3494.072718
X-RAY DIFFRACTIONr_mcbond_other3.3524.064717
X-RAY DIFFRACTIONr_mcangle_it4.986.068895
X-RAY DIFFRACTIONr_mcangle_other4.9776.077896
X-RAY DIFFRACTIONr_scbond_it3.8014.274665
X-RAY DIFFRACTIONr_scbond_other3.8094.281661
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8976.3968
X-RAY DIFFRACTIONr_long_range_B_refined9.20574.3886110
X-RAY DIFFRACTIONr_long_range_B_other9.20974.4256071
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 39 -
Rwork0.186 703 -
obs--88.97 %
Refinement TLS params.Method: refined / Origin x: 36.008 Å / Origin y: 13.854 Å / Origin z: 12.557 Å
111213212223313233
T0.0955 Å2-0.0315 Å2-0.0337 Å2-0.0431 Å20.0001 Å2--0.033 Å2
L0.8087 °2-0.2664 °2-0.3725 °2-0.1333 °2-0.005 °2--1.3411 °2
S-0.0005 Å °0.0394 Å °-0.0358 Å °0.0618 Å °-0.0479 Å °-0.0122 Å °-0.2545 Å °-0.0085 Å °0.0484 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 194
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION1A401 - 464

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