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- PDB-4nzy: Crystal structure (type-2) of dTMP kinase (st1543) from Sulfolobu... -

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Basic information

Entry
Database: PDB / ID: 4nzy
TitleCrystal structure (type-2) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7
ComponentsProbable thymidylate kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Probable thymidylate kinase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBiswas, A. / Jeyakanthan, J. / Sekar, K. / Kuramitsu, S. / Yokoyama, S.
CitationJournal: To be Published
Title: Insight into Substrate Binding Mechanism in Thymidylate Kinase based on Intrinsic Dynamics of the Active Site
Authors: Biswas, A. / Jeyakanthan, J. / Sekar, K.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Data collection
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable thymidylate kinase
B: Probable thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,61924
Polymers49,2632
Non-polymers2,35622
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint2 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.621, 62.643, 138.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable thymidylate kinase / dTMP kinase


Mass: 24631.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: Strain7 / Gene: STK_15430, tmk, tmk STK_15430 / Production host: Escherichia coli (E. coli) / References: UniProt: Q970Q8, dTMP kinase

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Non-polymers , 8 types, 195 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50% PEG 200, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K , temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Details: RH Coated Bent-Cyrindrical MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 25941 / Num. obs: 25941 / % possible obs: 99.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.53 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 28.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 6.42 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→26.01 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.087 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1218 5.1 %RANDOM
Rwork0.18301 ---
obs0.1857 22800 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.541 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å2-0 Å2-0 Å2
2---1.18 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.15→26.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 152 173 3571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023454
X-RAY DIFFRACTIONr_bond_other_d0.0010.023336
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9974634
X-RAY DIFFRACTIONr_angle_other_deg0.7237683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36524135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97715567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0781516
X-RAY DIFFRACTIONr_chiral_restr0.0620.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 71 -
Rwork0.194 1625 -
obs-1625 98.89 %

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