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- PDB-5xbh: Crystal structure of R145E mutant of thymidylate kinase (aq_969) ... -

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Basic information

Entry
Database: PDB / ID: 5xbh
TitleCrystal structure of R145E 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 / 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
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 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate kinase
B: Thymidylate kinase


Theoretical massNumber of molelcules
Total (without water)44,7502
Polymers44,7502
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-22 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.820, 51.550, 51.760
Angle α, β, γ (deg.)97.01, 105.90, 111.66
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 194 / Label seq-ID: 1 - 194

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Thymidylate kinase / dTMP kinase


Mass: 22374.881 Da / Num. of mol.: 2 / Mutation: R145E
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: 0.2M Ammonium acetate, 0.1M HEPES, 25% 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: May 26, 2016
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→48.2 Å / Num. obs: 17428 / % possible obs: 91.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1147 / CC1/2: 0.896 / % possible all: 64.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBR

2pbr


Resolution: 2.23→48.2 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.877 / SU B: 18.618 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.485 / ESU R Free: 0.286 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28113 838 4.8 %RANDOM
Rwork0.22871 ---
obs0.2312 16554 93.11 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 28.873 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.11 Å20.39 Å2
2---0.34 Å20.68 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.23→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 47 3185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193176
X-RAY DIFFRACTIONr_bond_other_d0.0030.023198
X-RAY DIFFRACTIONr_angle_refined_deg1.2062.0094256
X-RAY DIFFRACTIONr_angle_other_deg0.88737410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71324.595148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15515652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7841524
X-RAY DIFFRACTIONr_chiral_restr0.0670.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02622
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_it0.941.8321550
X-RAY DIFFRACTIONr_mcbond_other0.9371.8321549
X-RAY DIFFRACTIONr_mcangle_it1.5952.7441934
X-RAY DIFFRACTIONr_mcangle_other1.5952.7451935
X-RAY DIFFRACTIONr_scbond_it1.0381.981626
X-RAY DIFFRACTIONr_scbond_other1.0371.9811627
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7822.9092323
X-RAY DIFFRACTIONr_long_range_B_refined3.00221.2343462
X-RAY DIFFRACTIONr_long_range_B_other3.00221.2343462
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12312 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.229→2.287 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 48 -
Rwork0.488 1109 -
obs--84.27 %
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)
11.6147-0.289-0.30861.1639-0.93441.3983-0.02450.1823-0.0107-0.0008-0.0166-0.0049-0.0586-0.00880.04110.0586-0.0418-0.03270.05810.04650.0779-29.346-9.903-11.088
22.0768-0.00470.11651.2061-0.5130.5915-0.0606-0.13580.02720.04120.0066-0.01350.01570.00460.0540.04130.00220.00260.03080.03380.0604-37.268-38.03611.099
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 194
2X-RAY DIFFRACTION2B1 - 194

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