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- PDB-4s2e: Phosphate ion bound Crystal structure of thymidylate kinase (aq_9... -

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Basic information

Entry
Database: PDB / ID: 4s2e
TitlePhosphate ion bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
ComponentsThymidylate kinase
KeywordsTRANSFERASE / ATP binding / TMP binding
Function / homology
Function and homology information


dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytosol / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / 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
PHOSPHATE ION / Thymidylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBiswas, A. / Jeyakanthan, J. / Sekar, K.
CitationJournal: Febs J. / Year: 2017
Title: Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate.
Authors: Biswas, A. / Shukla, A. / Chaudhary, S.K. / Santhosh, R. / Jeyakanthan, J. / Sekar, K.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.title / _citation.year
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidylate kinase
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9964
Polymers44,8062
Non-polymers1902
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-38 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.870, 51.780, 53.650
Angle α, β, γ (deg.)92.29, 92.83, 112.76
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999993, -0.002154, -0.002994), (-0.002514, -0.195601, 0.98068), (-0.002698, 0.980681, 0.195595)-15.01078, 27.20847, -22.49747

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Components

#1: Protein Thymidylate kinase / / dTMP kinase


Mass: 22402.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_969, tmk / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: O67099, dTMP kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.1 M HEPES, 10% w/v Polyethylene glycol 8,000, 8% v/v Ethylene glycol , Microbatch Underoil, pH 7.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: Mirrors
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. all: 63136 / Num. obs: 15954 / % possible obs: 90.4 % / Redundancy: 4 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 9.6 / Num. unique all: 9345 / % possible all: 92.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBR

2pbr


Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.884 / SU B: 8.253 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.522 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26664 826 5.2 %RANDOM
Rwork0.20033 ---
obs0.20377 15094 90.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.711 Å2
Baniso -1Baniso -2Baniso -3
1--2.69 Å20.57 Å22.07 Å2
2--0.27 Å24.44 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 10 54 3051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193066
X-RAY DIFFRACTIONr_bond_other_d0.0020.023027
X-RAY DIFFRACTIONr_angle_refined_deg1.5232.0044134
X-RAY DIFFRACTIONr_angle_other_deg0.84736958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1224.427131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68615578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7851519
X-RAY DIFFRACTIONr_chiral_restr0.0760.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023381
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02642
X-RAY DIFFRACTIONr_mcbond_it2.3213.2391536
X-RAY DIFFRACTIONr_mcbond_other2.3223.2371535
X-RAY DIFFRACTIONr_mcangle_it3.4614.8511918
X-RAY DIFFRACTIONr_mcangle_other3.4614.8531919
X-RAY DIFFRACTIONr_scbond_it2.5813.4411530
X-RAY DIFFRACTIONr_scbond_other2.5553.4321521
X-RAY DIFFRACTIONr_scangle_other3.9775.0512201
X-RAY DIFFRACTIONr_long_range_B_refined5.43425.0163415
X-RAY DIFFRACTIONr_long_range_B_other5.43425.0243414
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 61 -
Rwork0.18 1126 -
obs--91.52 %

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