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Yorodumi- PDB-1qss: DDGTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qss | ||||||
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Title | DDGTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS | ||||||
Components |
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Keywords | Transferase/DNA / PROTEIN-DNA COMPLEX / CLOSED / Polymerase/DNA / Transferase-DNA COMPLEX | ||||||
Function / homology | Function and homology information nucleoside binding / hydrolase activity, acting on ester bonds / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Li, Y. / Mitaxov, V. / Waksman, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. Authors: Li, Y. / Mitaxov, V. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qss.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qss.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/1qss ftp://data.pdbj.org/pub/pdb/validation_reports/qs/1qss | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 3657.395 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4257.754 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 60865.879 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT / Mutation: A348E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: PWB254 / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 157 molecules
#4: Chemical | #5: Chemical | ChemComp-DG3 / | #6: 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: 2.23 Å3/Da / Density % sol: 44.74 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, SODIUM ACETATE, PEG 4000, MANGANESE CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / Details: Li, Y., (1998) EMBO J., 17, 7514. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 27317 / Num. obs: 27317 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.09 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.398 / % possible all: 95.5 |
Reflection | *PLUS % possible obs: 94.2 % / Num. measured all: 193699 / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 85.8 % |
-Processing
Software |
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Refinement | Resolution: 2.3→30 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.6 |