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- PDB-3v9p: Crystal structure of Thymidylate kinase from Burkholderia thailan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v9p | ||||||
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Title | Crystal structure of Thymidylate kinase from Burkholderia thailandensis | ||||||
![]() | Thymidylate kinase | ||||||
![]() | TRANSFERASE / SSGCID / Thymidylate kinase / Burkholderia thailandensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.2 KB | Display | ![]() |
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PDB format | ![]() | 137.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.9 KB | Display | ![]() |
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Full document | ![]() | 471.4 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3d63C ![]() 3dahC ![]() 3eizC ![]() 3ej2C ![]() 3ek2C ![]() 3ezoC ![]() 3f0fC ![]() 3ftpC ![]() 3gk0C ![]() 3gk3C ![]() 3gvfC ![]() 3gwaC ![]() 3gweC ![]() 3imlC ![]() 3sz8C ![]() 3t4cC ![]() 3tmlC ![]() 3tmqC ![]() 3txyC ![]() 3u7jC ![]() 3ue9C ![]() 3uk1C ![]() 3uk2C ![]() 3undC ![]() 3uptC ![]() 3urrC ![]() 3uw1C ![]() 3uw2C ![]() 3uw3C ![]() 3v2iC ![]() 3v7nC ![]() 3v8hC ![]() 3v9oC ![]() 3vavC ![]() 4ddoC ![]() 4dfeC ![]() 4dheC ![]() 4dhkC ![]() 4dutC ![]() 4dz4C ![]() 4e4tC ![]() 4efiC ![]() 4eg0C ![]() 4egjC ![]() 4ek2C ![]() 4eqyC ![]() 4ewgC ![]() 4exqC ![]() 4f2gC ![]() 4f32C ![]() 4f3nC ![]() 4f3yC ![]() 4f4hC ![]() 4f7dC ![]() 4fk8C ![]() 4fryC ![]() 4g1kC ![]() 4g67C ![]() 4ghkC ![]() 4h3yC ![]() 4h3zC ![]() 4h4gC ![]() 3ld9S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25405.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 267 molecules ![](data/chem/img/MRD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 11, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: RIGAKU MICROMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.99 Å2 / Biso mean: 20.9104 Å2 / Biso min: 7.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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