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Yorodumi- PDB-3akd: Crystal structure of CMP kinase in complex with CDP from Thermus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3akd | ||||||
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Title | Crystal structure of CMP kinase in complex with CDP from Thermus thermophilus HB8 | ||||||
Components | Cytidylate kinase | ||||||
Keywords | TRANSFERASE / CMP kinase / CDP complex / open conformation / nucleotide metabolism | ||||||
Function / homology | Function and homology information (d)CMP kinase / CMP kinase activity / dCMP kinase activity / pyrimidine nucleotide metabolic process / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mega, R. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | ||||||
Citation | Journal: To be Published Title: The crystal structure of the tertiary complex of CMP kinase with a phosphoryl group acceptor and a donor from Thermus thermophilus HB8 Authors: Mega, R. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3akd.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3akd.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 3akd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/3akd ftp://data.pdbj.org/pub/pdb/validation_reports/ak/3akd | HTTPS FTP |
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-Related structure data
Related structure data | 3akcC 2cmkS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 22584.818 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): BL21(DE3) / References: UniProt: Q5SL35, UMP/CMP kinase |
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#2: Chemical | ChemComp-CDP / |
#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: 2.72 Å3/Da / Density % sol: 54.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M BIS-TRIS propane, 3.5M sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 6, 2006 |
Radiation | Monochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 29707 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 53 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1768 / % possible all: 55.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CMK Resolution: 1.6→38.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1453360.21 / 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: 43.9677 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→38.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016
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Xplor file |
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