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Yorodumi- PDB-3sz5: Crystal Structure of LHK-Exo in complex with 5-phosphorylated oli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sz5 | ||||||
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Title | Crystal Structure of LHK-Exo in complex with 5-phosphorylated oligothymidine (dT)4 | ||||||
Components |
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Keywords | HYDROLASE/DNA / alkaline exonuclease / digest double stranded DNA / strict 5-3-polarity / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Laribacter hongkongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Yang, W. / Chen, W.Y. / Wang, H. / Zhang, Q. / Zhou, W. / Bartlam, M. / Watt, R.M. / Rao, Z. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis. Authors: Yang, W. / Chen, W.Y. / Wang, H. / Ho, J.W. / Huang, J.D. / Woo, P.C. / Lau, S.K. / Yuen, K.Y. / Zhang, Q. / Zhou, W. / Bartlam, M. / Watt, R.M. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sz5.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sz5.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 3sz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/3sz5 ftp://data.pdbj.org/pub/pdb/validation_reports/sz/3sz5 | HTTPS FTP |
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-Related structure data
Related structure data | 3syySC 3sz4C 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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-Components
#1: Protein | Mass: 24476.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Laribacter hongkongensis (bacteria) / Strain: HLHK9 / Gene: LHK_01497 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1D7P6 |
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#2: DNA chain | Mass: 1171.814 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 0.1M Tris pH 8.4, 1.0M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 2, 2010 / 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: 2.8→50 Å / Num. all: 8207 / Num. obs: 8198 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 35.5 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.4 / Num. unique all: 397 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SYY Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.799→2.871 Å / Total num. of bins used: 20
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