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- PDB-5h5k: ATP and CMP bound Crystal structure of thymidylate kinase (aq_969... -

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Basic information

Entry
Database: PDB / ID: 5h5k
TitleATP and CMP 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'-TRIPHOSPHATE / CYTIDINE-5'-MONOPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionNov 6, 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_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.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.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.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

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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)46,70111
Polymers44,8062
Non-polymers1,8969
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-43.7 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.840, 51.863, 53.595
Angle α, β, γ (deg.)92.00, 92.30, 112.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 195
2111B1 - 195

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1, -0.000759, -4.0E-6), (0.000144, -0.195131, 0.980777), (-0.000745, 0.980777, 0.195131)22.60571, 30.31996, -24.71533

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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 , 5 types, 72 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 0.1M HEPES, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol

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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: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 18641 / % possible obs: 98.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 6.83
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.21 / % possible all: 98.2

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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: 2.3→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.395 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25109 939 5.1 %RANDOM
Rwork0.19449 ---
obs0.19743 17588 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.468 Å2
Baniso -1Baniso -2Baniso -3
1--2.94 Å20.78 Å22.41 Å2
2--1.31 Å24.65 Å2
3----0.56 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 118 63 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193159
X-RAY DIFFRACTIONr_bond_other_d0.0020.023074
X-RAY DIFFRACTIONr_angle_refined_deg1.6692.0424275
X-RAY DIFFRACTIONr_angle_other_deg0.96837058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31324.228123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02615570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2211519
X-RAY DIFFRACTIONr_chiral_restr0.080.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02656
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_it2.5083.8941546
X-RAY DIFFRACTIONr_mcbond_other2.5083.8911545
X-RAY DIFFRACTIONr_mcangle_it3.7735.831930
X-RAY DIFFRACTIONr_mcangle_other3.7725.8331931
X-RAY DIFFRACTIONr_scbond_it3.1154.2741613
X-RAY DIFFRACTIONr_scbond_other3.1084.2681609
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6456.3122338
X-RAY DIFFRACTIONr_long_range_B_refined6.07146.1653476
X-RAY DIFFRACTIONr_long_range_B_other6.07146.1813477
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 2911 / Type: tight thermal / Rms dev position: 4.02 Å / Weight position: 0.5
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 57 -
Rwork0.285 1269 -
obs--94.44 %

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