+Open data
-Basic information
Entry | Database: PDB / ID: 2cck | ||||||
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Title | CRYSTAL STRUCTURE OF UNLIGANDED S. AUREUS THYMIDYLATE KINASE | ||||||
Components | THYMIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / KINASE / NUCLEOTIDE BIOSYNTHESIS / TMP-BINDING / ATP-BINDING / THYMIDYLATE KINASE | ||||||
Function / homology | Function and homology information dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Kotaka, M. / Dhaliwal, B. / Ren, J. / Nichols, C.E. / Angell, R. / Lockyer, M. / Hawkins, A.R. / Stammers, D.K. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Structures of S. Aureus Thymidylate Kinase Reveal an Atypical Active Site Configuration and an Intermediate Conformational State Upon Substrate Binding Authors: Kotaka, M. / Dhaliwal, B. / Ren, J. / Nichols, C.E. / Angell, R. / Lockyer, M. / Hawkins, A.R. / Stammers, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cck.cif.gz | 93.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cck.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 2cck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cck_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 2cck_full_validation.pdf.gz | 456.6 KB | Display | |
Data in XML | 2cck_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 2cck_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/2cck ftp://data.pdbj.org/pub/pdb/validation_reports/cc/2cck | HTTPS FTP |
-Related structure data
Related structure data | 2ccgSC 2ccjC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.1409, 0.25088, 0.955771), Vector: |
-Components
#1: Protein | Mass: 23454.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P65248, dTMP kinase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 43.9 % |
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Crystal grow | pH: 7.2 Details: 1M LICL, 0.1M NA CACODYLATE, PH7.2, 16% PEG 6000, pH 7.20 |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 18, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 19676 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 50.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 18 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CCG Resolution: 2.21→22.71 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 702447.31 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.0907 Å2 / ksol: 0.36682 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.21→22.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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