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Yorodumi- PDB-3kd6: Crystal Structure of Nucleoside Kinase from Chlorobium tepidum in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kd6 | ||||||
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Title | Crystal Structure of Nucleoside Kinase from Chlorobium tepidum in Complex with AMP | ||||||
Components | Carbohydrate kinase, PfkB family | ||||||
Keywords | TRANSFERASE / KINASE / PFKB / NUCLEOSIDE KINASE / AMP / PSI-II / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlorobaculum tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å | ||||||
Authors | Satyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Nucleoside Kinase from Chlorobium tepidum in Complex with AMP Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kd6.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kd6.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kd6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3kd6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3kd6_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 3kd6_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/3kd6 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/3kd6 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35472.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: TOP10 (Invitrogen) / Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: CT0976 / Plasmid: pSGX32 (BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) Codon+RIL / References: UniProt: Q8KDR9 #2: Chemical | #3: Chemical | #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: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M SODIUM CHLORIDE 0.1M BIS-TRIS pH 5.5 20% PEG 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. all: 51078 / Num. obs: 51078 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.139 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 4975 / Rsym value: 0.6 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.88→46.87 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.88→46.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→2 Å / Rfactor Rfree error: 0.014
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