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- PDB-3n2i: 2.25 Angstrom resolution crystal structure of a thymidylate kinas... -

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Basic information

Entry
Database: PDB / ID: 3n2i
Title2.25 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with thymidine
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Thymidylate Kinase / Vibrio cholerae / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / ATP-binding / Kinase / Nucleotide biosynthesis / Nucleotide-binding / CSGID
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
THYMIDINE / Thymidylate kinase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHalavaty, A.S. / Minasov, G. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.25 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with thymidine
Authors: Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Thymidylate kinase
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4336
Polymers52,8782
Non-polymers5554
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-35 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 92.600, 231.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Thymidylate kinase / dTMP kinase


Mass: 26438.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria)
Strain: N16961 / Gene: tmk, VC_2016 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / References: UniProt: Q9KQI2, dTMP kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7.0 mg/mL protein in 10 mM Tris/HCl pH 8.3 0.25 M NaCl, 5 mM BME. Crystallization condition is The PACT Suite (#34). Crystals grew from 1:1 v/v drop, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2010 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 24340 / Num. obs: 24340 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 40.13
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1176 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LV8

3lv8


Resolution: 2.25→29.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.58 / SU ML: 0.148 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26109 1239 5.1 %RANDOM
Rwork0.2058 ---
obs0.20846 23074 99.88 %-
all-23074 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 69.842 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å2-0 Å2-0 Å2
2--2.26 Å20 Å2
3----4.52 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 36 77 3363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223334
X-RAY DIFFRACTIONr_bond_other_d0.0010.022281
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9864505
X-RAY DIFFRACTIONr_angle_other_deg0.9835564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4085414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62624.601163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45915611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1961531
X-RAY DIFFRACTIONr_chiral_restr0.0940.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02634
X-RAY DIFFRACTIONr_mcbond_it0.6311.52059
X-RAY DIFFRACTIONr_mcbond_other0.1651.5849
X-RAY DIFFRACTIONr_mcangle_it1.17323304
X-RAY DIFFRACTIONr_scbond_it2.10231275
X-RAY DIFFRACTIONr_scangle_it3.4494.51201
LS refinement shellResolution: 2.251→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 86 -
Rwork0.289 1653 -
obs-1653 99.77 %
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)
10.61780.1441-0.62093.8357-0.24333.63380.1171-0.15-0.1006-0.4982-0.46950.08980.59260.8210.35240.30160.31050.0370.56660.08410.28933.8818-31.101911.444
22.0745-0.4966-0.46710.0285-4.39614.56220.33160.11970.0105-0.6068-0.33920.3495-0.00450.27930.00760.1170.1106-0.0060.4304-0.02530.181529.6579-17.921513.4129
30.4785-0.428-0.65393.7626-1.07583.38350.2536-0.16350.158-0.3122-0.517-0.4293-0.21141.00020.26340.18870.10120.09580.760.12460.344841.1947-18.386511.1713
42.9094-1.13913.91188.0127-3.72717.36790.2365-0.15280.0904-1.2589-0.5135-0.42350.44460.80370.2770.43680.22050.22250.89350.14990.392842.8875-19.24811.081
51.69131.028-3.88526.18032.272922.81330.0302-0.3944-0.1253-0.1131-0.4611-0.41950.32561.77650.43090.47830.70170.21721.15660.3250.559248.1873-38.11737.7076
61.6352-1.0076-0.39273.73410.20472.69180.19460.22810.0955-0.4211-0.43270.7602-0.7541-0.17220.23820.32740.1793-0.07310.2929-0.0730.415714.50387.968113.3865
71.3327-2.76770.58088.3256-0.77574.96750.09990.0319-0.1579-0.1805-0.44350.6361-0.0681-0.14560.34360.05050.08180.01540.2802-0.06950.223622.3636-7.472415.7082
81.7736-1.0388-0.314.7503-0.80892.85780.2142-0.06750.20680.1447-0.32250.251-0.64380.18880.10830.19680.01520.01810.2219-0.04450.239820.75373.381822.3112
97.0472.2454-0.10199.4736-1.01513.3641-0.1507-0.426-0.41760.2215-0.18470.6266-0.42920.10680.33540.25380.02610.14690.3211-0.09280.366115.8301-0.790729.3486
1010.09643.4944-3.282412.173-5.36877.14130.57130.19260.77740.8029-0.16341.2701-1.8023-0.6041-0.40790.78170.22880.13640.3767-0.20710.7211.365219.519624.0235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 53
2X-RAY DIFFRACTION2A54 - 93
3X-RAY DIFFRACTION3A94 - 144
4X-RAY DIFFRACTION4A145 - 185
5X-RAY DIFFRACTION5A186 - 208
6X-RAY DIFFRACTION6B2 - 52
7X-RAY DIFFRACTION7B53 - 86
8X-RAY DIFFRACTION8B87 - 149
9X-RAY DIFFRACTION9B150 - 183
10X-RAY DIFFRACTION10B184 - 210

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