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Yorodumi- PDB-3lv8: 1.8 Angstrom resolution crystal structure of a thymidylate kinase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lv8 | ||||||
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Title | 1.8 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with TMP, thymidine-5'-diphosphate and ADP | ||||||
Components | Thymidylate kinase | ||||||
Keywords | TRANSFERASE / 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 / phosphorylation / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar eltor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: 1.8 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with TMP, thymidine-5'-diphosphate and ADP Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lv8.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lv8.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 3lv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lv8_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3lv8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3lv8_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 3lv8_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/3lv8 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/3lv8 | HTTPS FTP |
-Related structure data
Related structure data | 4tmkS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26438.818 Da / Num. of mol.: 1 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 |
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-Non-polymers , 6 types, 297 molecules
#2: Chemical | ChemComp-ADP / | ||||
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#3: Chemical | ChemComp-TMP / | ||||
#4: Chemical | ChemComp-TYD / | ||||
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 7mg/mL protein; The PACT Suite condition #47 (D11), pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2010 / Details: Beryllium lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 23299 / Num. obs: 23299 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1089 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TMK Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.665 / SU ML: 0.07 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.439 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 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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