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- PDB-3v9p: Crystal structure of Thymidylate kinase from Burkholderia thailan... -

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Basic information

Entry
Database: PDB / ID: 3v9p
TitleCrystal structure of Thymidylate kinase from Burkholderia thailandensis
ComponentsThymidylate kinase
KeywordsTRANSFERASE / SSGCID / Thymidylate kinase / Burkholderia thailandensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding
Similarity search - Function
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Thymidylate kinase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionDec 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 13, 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)51,4569
Polymers50,8122
Non-polymers6457
Water4,684260
1
A: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7675
Polymers25,4061
Non-polymers3614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6894
Polymers25,4061
Non-polymers2833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Thymidylate kinase
hetero molecules

B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4569
Polymers50,8122
Non-polymers6457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area3880 Å2
ΔGint-40 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.130, 77.970, 84.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thymidylate kinase / / dTMP kinase


Mass: 25405.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I2154, tmk, YP_442675.1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SWM4, dTMP kinase

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Non-polymers , 5 types, 267 molecules

#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: EBS Wizard 3/4 screen h6: 30% MPD, 25% PEG 1500, 100mM HOAc/NAOAC; protein ButhA.01616.a.A1 PS01176 at 56.3 mg/ml, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 11, 2011
RadiationMonochromator: RIGAKU MICROMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 35992 / Num. obs: 35693 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.96 % / Biso Wilson estimate: 24.144 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsRsym value% possible all
1.9-1.952.70.5272.36616261624540.52793.8
1.95-20.4513.579477249897.2
2-2.060.4024.2910617245299
2.06-2.120.3375.4211596241399.6
2.12-2.190.2617.2712354233199.8
2.19-2.270.2278.61126772266100
2.27-2.360.2069.6813569220899.9
2.36-2.450.19111.4614845210399.8
2.45-2.560.17112.37145822033100
2.56-2.690.15613.1913930193799.9
2.69-2.830.12415.9713543187299.9
2.83-30.10417.5412684175899.9
3-3.210.08520.612025165999.9
3.21-3.470.06326.2411193155299.9
3.47-3.80.04636.11103421445100
3.8-4.250.03940.919250129699.8
4.25-4.910.035458272117299.8
4.91-6.010.04234.44703399299.9
6.01-8.50.0434.715424790100
8.50.02356.82287946298.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3LD9

3ld9


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1785 / WRfactor Rwork: 0.1485 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8573 / SU B: 5.852 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1457 / SU Rfree: 0.1345 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1786 5 %RANDOM
Rwork0.1814 ---
all0.1833 35992 --
obs0.1833 33908 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.99 Å2 / Biso mean: 20.9104 Å2 / Biso min: 7.91 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å2-0 Å2-0 Å2
2---0.44 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 43 260 3415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193254
X-RAY DIFFRACTIONr_bond_other_d0.0010.022300
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9734406
X-RAY DIFFRACTIONr_angle_other_deg0.90435510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93321.899158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40815519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1491544
X-RAY DIFFRACTIONr_chiral_restr0.0820.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02735
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 126 -
Rwork0.261 2168 -
all-2294 -
obs-2454 93.37 %
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)
10.22590.1377-0.05570.5471-0.38150.8154-0.0072-0.00480.0105-0.0313-0.02690.0067-0.1332-0.03190.03410.14780.00970.00010.00710.00060.053122.81769.04611.486
20.14280.13790.10821.60090.73430.6474-0.0127-0.0002-0.012-0.2526-0.04710.0388-0.090.00440.05980.13170.01320.01330.004-0.00020.045946.05386.65-1.358
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 206
2X-RAY DIFFRACTION1A250 - 255
3X-RAY DIFFRACTION2B2 - 206
4X-RAY DIFFRACTION2B250 - 255

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