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- PDB-4rzx: Crystal structure (type-3) of dTMP kinase (st1543) from Sulfolobu... -

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Basic information

Entry
Database: PDB / ID: 4rzx
TitleCrystal structure (type-3) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7
ComponentsProbable thymidylate kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
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
NICKEL (II) ION / PHOSPHATE ION / Probable thymidylate kinase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBiswas, A. / Jeyakanthan, J. / Sekar, K.
CitationJournal: To be Published
Title: Crystal structure (type-3) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7
Authors: Biswas, A. / Jeyakanthan, J. / Sekar, K.
History
DepositionDec 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_site
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.ptnr1_label_seq_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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable thymidylate kinase
B: Probable thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5125
Polymers49,2632
Non-polymers2493
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-36 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.934, 63.222, 138.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable thymidylate kinase / dTMP kinase


Mass: 24631.482 Da / Num. of mol.: 2 / Fragment: Thymidylate Kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: Strain7 / Gene: STK_15430, tmk / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q970Q8, dTMP kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 0.01 M Magnesium chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.1 M HEPES sodium, 15% w/v Polyethylene glycol 3,350, 0.5 M Sodium fluoride, pH 7.0, Microbatch Underoil, ...Details: 0.01 M Magnesium chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.1 M HEPES sodium, 15% w/v Polyethylene glycol 3,350, 0.5 M Sodium fluoride, pH 7.0, Microbatch Underoil, temperature 293.0K, EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Details: RH Coated Bent-Cyrindrical MIRROR
RadiationMonochromator: SI-1 1 1 Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20021 / % possible obs: 99 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.348
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 4.66 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PLR

2plr


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.8 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25903 1031 5.2 %RANDOM
Rwork0.2011 ---
obs0.20415 18955 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.449 Å2
Baniso -1Baniso -2Baniso -3
1-3.06 Å20 Å20 Å2
2---0.92 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 11 16 3164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023222
X-RAY DIFFRACTIONr_bond_other_d0.0010.023010
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9674384
X-RAY DIFFRACTIONr_angle_other_deg0.85536887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95823.359131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59315511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8151518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
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_it3.764.5061621
X-RAY DIFFRACTIONr_mcbond_other3.7594.5051620
X-RAY DIFFRACTIONr_mcangle_it5.3056.7342018
X-RAY DIFFRACTIONr_mcangle_other5.35372019
X-RAY DIFFRACTIONr_scbond_it4.0694.731601
X-RAY DIFFRACTIONr_scbond_other4.2224.931612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1257.2412376
X-RAY DIFFRACTIONr_long_range_B_refined8.09937.5763830
X-RAY DIFFRACTIONr_long_range_B_other8.137.573829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 82 -
Rwork0.22 1364 -
obs--98.64 %
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)
11.44191.2004-0.8572.8368-1.14270.61160.1343-0.14480.11030.3796-0.0680.0875-0.16050.0601-0.06630.31360.0401-0.01130.1728-0.04960.2388-33.289-1.19524.018
22.5084-0.1483-1.25661.76280.08892.2192-0.1543-0.07690.0412-0.05160.1033-0.18420.2092-0.02880.0510.2077-0.05670.02030.0611-0.02540.1392-12.2851.242-2.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 59
2X-RAY DIFFRACTION1A144 - 183
3X-RAY DIFFRACTION2B32 - 43
4X-RAY DIFFRACTION2B44 - 77
5X-RAY DIFFRACTION2B78 - 94
6X-RAY DIFFRACTION2B95 - 183
7X-RAY DIFFRACTION2B184 - 208

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