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- PDB-5h5b: Citrate ion bound crystal structure of thymidylate kinase (aq_969... -

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Basic information

Entry
Database: PDB / ID: 5h5b
TitleCitrate ion 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 / 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
CITRATE ANION / Thymidylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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 5, 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 / 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)45,1844
Polymers44,8062
Non-polymers3782
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-17 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.760, 51.530, 53.250
Angle α, β, γ (deg.)92.85, 92.49, 112.63
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
1114A1 - 195
2114B1 - 195

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99998, 0.000127, -0.006274), (-0.006161, -0.210083, 0.977664), (-0.001194, 0.977684, 0.210079)-44.61343, -22.51073, 29.4277

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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 (strain VF5) (bacteria)
Strain: VF5 / Gene: tmk, aq_969 / Production host: Escherichia coli (E. coli) / References: UniProt: O67099, dTMP kinase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→53.06 Å / Num. obs: 24537 / % possible obs: 91.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 33.8 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 2.03→2.09 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1170 / CC1/2: 0.92 / % possible all: 60.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBR

2pbr


Resolution: 2.05→53.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.656 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.213 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27135 1251 5.1 %RANDOM
Rwork0.21015 ---
obs0.21331 23283 93.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.369 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å20.26 Å22.29 Å2
2--0.72 Å24.7 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.05→53.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 26 97 3153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193092
X-RAY DIFFRACTIONr_bond_other_d0.0010.023067
X-RAY DIFFRACTIONr_angle_refined_deg1.2852.014162
X-RAY DIFFRACTIONr_angle_other_deg0.92237043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9225385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66624.351131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04215587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8481521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02639
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_it1.7023.6111546
X-RAY DIFFRACTIONr_mcbond_other1.6963.6081545
X-RAY DIFFRACTIONr_mcangle_it2.695.4091929
X-RAY DIFFRACTIONr_mcangle_other2.6925.4111930
X-RAY DIFFRACTIONr_scbond_it1.873.8311546
X-RAY DIFFRACTIONr_scbond_other1.873.8331547
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9955.6642233
X-RAY DIFFRACTIONr_long_range_B_refined4.48242.5823372
X-RAY DIFFRACTIONr_long_range_B_other4.48442.6013373
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2981 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.260.5
Bmedium thermal3.762
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 101 -
Rwork0.321 1531 -
obs--85.18 %

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