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- PDB-5xb2: ADP-Mg-F-dTMP bound Crystal structure of thymidylate kinase (aq_9... -

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Basic information

Entry
Database: PDB / ID: 5xb2
TitleADP-Mg-F-dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Kinase / Tranferase / Complex / Nucleotide Binding
Function / homology
Function and homology information


dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / ATP binding / cytoplasm / cytosol
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FLUORIDE ION / THYMIDINE-5'-PHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.161 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
DepositionMar 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,38610
Polymers44,8062
Non-polymers1,5808
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-44 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.620, 52.990, 54.019
Angle α, β, γ (deg.)88.90, 90.83, 70.53
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules BA

#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 (strain VF5) (bacteria)
Strain: VF5 / Gene: tmk, aq_969 / Production host: Escherichia coli (E. coli) / References: UniProt: O67099, dTMP kinase

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Non-polymers , 5 types, 151 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: F
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.57 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7
Details: 0.2M Ammonium citrate tribasic, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97372 Å / Relative weight: 1
ReflectionResolution: 2.16→54 Å / Num. obs: 23220 / % possible obs: 97.3 % / Redundancy: 4 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.944 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3080 / CC1/2: 0.64 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBR

2pbr


Resolution: 2.161→49.944 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.06
RfactorNum. reflection% reflection
Rfree0.2587 1174 5.06 %
Rwork0.1951 --
obs0.1985 23182 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.161→49.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 100 143 3298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073230
X-RAY DIFFRACTIONf_angle_d1.0094369
X-RAY DIFFRACTIONf_dihedral_angle_d17.9751959
X-RAY DIFFRACTIONf_chiral_restr0.049507
X-RAY DIFFRACTIONf_plane_restr0.005541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.161-2.25930.41651060.33832491X-RAY DIFFRACTION87
2.2593-2.37850.3941320.25382772X-RAY DIFFRACTION97
2.3785-2.52750.33441490.22462788X-RAY DIFFRACTION98
2.5275-2.72260.33171450.21592792X-RAY DIFFRACTION99
2.7226-2.99660.30571460.20742792X-RAY DIFFRACTION99
2.9966-3.43010.22181580.19372784X-RAY DIFFRACTION99
3.4301-4.32120.21391690.15262797X-RAY DIFFRACTION99
4.3212-49.95690.18841690.14552792X-RAY DIFFRACTION99

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