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Yorodumi- PDB-3w8n: Open form structure of CMP kinase in complex with CMP from Thermu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w8n | ||||||
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Title | Open form structure of CMP kinase in complex with CMP from Thermus thermophilus HB8 | ||||||
Components | Cytidylate kinase | ||||||
Keywords | TRANSFERASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / kinase / CMP | ||||||
Function / homology | Function and homology information (d)CMP kinase / CMP kinase activity / dCMP kinase activity / : / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Nakagawa, N. / Mega, R. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of CMP kinase: insights into initial substrate recognition and reaction mechanisms Authors: Mega, R. / Nakagawa, N. / Masui, R. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w8n.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w8n.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 3w8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w8n_validation.pdf.gz | 785.8 KB | Display | wwPDB validaton report |
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Full document | 3w8n_full_validation.pdf.gz | 786.2 KB | Display | |
Data in XML | 3w8n_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3w8n_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/3w8n ftp://data.pdbj.org/pub/pdb/validation_reports/w8/3w8n | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22725.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0458 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SL35, (d)CMP kinase |
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#2: Chemical | ChemComp-C5P / |
#3: 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: 3.02 Å3/Da / Density % sol: 59.22 % / Mosaicity: 0.354 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10mM CMP, 10mM MgCl2, 0.6M sodium succinate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 10, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: transparent double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av σ(I) over netI: 20.39 / Number: 52425 / Rmerge(I) obs: 0.049 / Χ2: 1.77 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 26811 / % possible obs: 99.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.2→50 Å / Num. obs: 26811 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.049 / Χ2: 1.767 / Net I/σ(I): 23.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0 / Reflection: 12904 / Reflection acentric: 12904 / Reflection centric: 0 | |||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→42.62 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8396 / Data cutoff high absF: 821362 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.7231 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85 Å2 / Biso mean: 37.6258 Å2 / Biso min: 18.16 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→42.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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