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- PDB-5xb5: Crystal structure of R90A mutant of thymidylate kinase (aq_969) f... -

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Basic information

Entry
Database: PDB / ID: 5xb5
TitleCrystal structure of R90A mutant of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Kinase / Complex / Nucleotide 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: 2.23 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.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,8244
Polymers44,6342
Non-polymers1902
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-36 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.010, 51.840, 53.640
Angle α, β, γ (deg.)92.17, 92.67, 112.83
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(-0.999992, -0.003523, -0.00208), (-0.001378, -0.188573, 0.982058), (-0.003852, 0.982053, 0.188567)40.56262, 27.40212, -22.39915

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Components

#1: Protein Thymidylate kinase / / dTMP kinase


Mass: 22316.844 Da / Num. of mol.: 2 / Mutation: R90A
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-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.: 38 / 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: 50.05 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2012
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→53.48 Å / Num. obs: 19751 / % possible obs: 93 % / Redundancy: 4.3 % / Biso Wilson estimate: 28.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1347 / CC1/2: 0.851 / % possible all: 68.6

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Processing

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

2pbr


Resolution: 2.23→53.48 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.873 / SU B: 27.129 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.265 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28591 991 5 %RANDOM
Rwork0.24035 ---
obs0.24266 18753 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.258 Å2
Baniso -1Baniso -2Baniso -3
1--6.6 Å22.88 Å2-0.2 Å2
2--4.73 Å22.66 Å2
3----2.7 Å2
Refinement stepCycle: 1 / Resolution: 2.23→53.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 10 38 3022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193019
X-RAY DIFFRACTIONr_bond_other_d0.0030.022989
X-RAY DIFFRACTIONr_angle_refined_deg1.8552.0064066
X-RAY DIFFRACTIONr_angle_other_deg1.13636873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3545381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.17125124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44115568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8441515
X-RAY DIFFRACTIONr_chiral_restr0.1060.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023316
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02611
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_it0.5580.7891533
X-RAY DIFFRACTIONr_mcbond_other0.5560.7871532
X-RAY DIFFRACTIONr_mcangle_it1.0241.1781911
X-RAY DIFFRACTIONr_mcangle_other1.0241.181912
X-RAY DIFFRACTIONr_scbond_it0.5460.8131486
X-RAY DIFFRACTIONr_scbond_other0.5450.8151487
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.891.2192156
X-RAY DIFFRACTIONr_long_range_B_refined4.9029.1073308
X-RAY DIFFRACTIONr_long_range_B_other4.9029.1093308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 2879 / Type: tight thermal / Rms dev position: 3.16 Å / Weight position: 0.5
LS refinement shellResolution: 2.23→2.287 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 67 -
Rwork0.353 1319 -
obs--89.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3849-0.2189-0.39120.9166-0.45930.3241-0.2179-0.2175-0.60170.03840.0786-0.0682-0.0887-0.01070.13930.6088-0.00610.0920.0322-0.03440.438716.347919.195222.5622
23.59040.5755-0.65051.7201-1.85582.0793-0.72191.42671.19190.11930.3154-0.21440.0847-0.27170.40660.7778-0.3449-0.06550.60240.52330.742824.25445.61520.6232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 193
2X-RAY DIFFRACTION2B1 - 192

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