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- PDB-5h56: ADP and dTDP bound Crystal structure of thymidylate kinase (aq_96... -

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Basic information

Entry
Database: PDB / ID: 5h56
TitleADP and dTDP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Kinase / Rossmann Fold / Product-bound
Function / homology
Function and homology information


dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / THYMIDINE-5'-DIPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBiswas, A. / Jeyakanthan, J. / Sekar, K. / Kuramitsu, S. / Yokoyama, S.
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
DepositionNov 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)46,92716
Polymers44,8062
Non-polymers2,12114
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-145 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.482, 62.414, 76.144
Angle α, β, γ (deg.)90.00, 91.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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 , 6 types, 330 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-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 45% MPD, 0.2M CaCl2, 10mM Mg, 10mM dTDP, 10mM ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Sep 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 42940 / % possible obs: 97.8 % / Redundancy: 7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 45.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 7.51 / Num. unique all: 3578 / % possible all: 82.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBR

2pbr


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.657 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18525 2127 5 %RANDOM
Rwork0.15589 ---
obs0.15736 40793 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.35 Å2
2--1.02 Å20 Å2
3----0.93 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 128 316 3517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193361
X-RAY DIFFRACTIONr_bond_other_d0.0020.023357
X-RAY DIFFRACTIONr_angle_refined_deg1.5692.0484562
X-RAY DIFFRACTIONr_angle_other_deg0.91137761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1615426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20524.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81315662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.361523
X-RAY DIFFRACTIONr_chiral_restr0.0810.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
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_it0.8751.2871594
X-RAY DIFFRACTIONr_mcbond_other0.8691.2851593
X-RAY DIFFRACTIONr_mcangle_it1.4281.9231999
X-RAY DIFFRACTIONr_mcangle_other1.4291.9262000
X-RAY DIFFRACTIONr_scbond_it1.4221.4561767
X-RAY DIFFRACTIONr_scbond_other1.4221.4581768
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.252.122545
X-RAY DIFFRACTIONr_long_range_B_refined3.86215.6213831
X-RAY DIFFRACTIONr_long_range_B_other3.86215.6323832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 120 -
Rwork0.187 2418 -
obs--79.66 %

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