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Yorodumi- PDB-3a4k: Crystal structural analysis of HindIII restriction endonuclease i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a4k | ||||||
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Title | Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution | ||||||
Components |
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Keywords | HYDROLASE/DNA / Type II restriction enzyme HindIII(E.C.3.1.21.4)/DNA / hydrolase-DNA COMPLEX / Endonuclease / Hydrolase / Nuclease / Restriction system | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Watanabe, N. / Sato, C. / Takasaki, Y. / Tanaka, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations Authors: Watanabe, N. / Takasaki, Y. / Sato, C. / Ando, S. / Tanaka, I. | ||||||
History |
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Remark 650 | HELIX Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a4k.cif.gz | 305.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a4k.ent.gz | 241.3 KB | Display | PDB format |
PDBx/mmJSON format | 3a4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a4k_validation.pdf.gz | 527.3 KB | Display | wwPDB validaton report |
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Full document | 3a4k_full_validation.pdf.gz | 553.4 KB | Display | |
Data in XML | 3a4k_validation.xml.gz | 51.7 KB | Display | |
Data in CIF | 3a4k_validation.cif.gz | 74.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/3a4k ftp://data.pdbj.org/pub/pdb/validation_reports/a4/3a4k | HTTPS FTP |
-Related structure data
Related structure data | 2e52SC 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ACBD
#1: Protein | Mass: 35136.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: hindIIIR / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS References: UniProt: P43870, type II site-specific deoxyribonuclease |
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-DNA chain , 3 types, 10 molecules EGIKFHJLMN
#2: DNA chain | Mass: 1175.819 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: 5'-fragment of cleaved cognate DNA with HindIIIR #3: DNA chain | Mass: 2442.616 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: 3'-fragment of cleaved cognate DNA with HindIIIR #4: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This DNA sequence synthesized chemically contains cognate HindIIIR recognition sequence and elongated scaffolds on both sides |
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-Non-polymers , 5 types, 587 molecules
#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-MN / #7: Chemical | #8: Chemical | ChemComp-ACT / #9: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | MG ION WAS USED IN THE EXPERIMENT, BUT METAL IONS AT SITES O, P, Q AND R IN THE STRUCTURE HAVE BEEN ...MG ION WAS USED IN THE EXPERIMENT |
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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: 2.99 Å3/Da / Density % sol: 58.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG3350, ammonium acetate, Magnesium ion, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 20, 2006 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 100664 / % possible obs: 99.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 2.17→2.23 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.5 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E52 Resolution: 2.17→41.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.791 / SU ML: 0.125 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.53 Å2 / Biso mean: 36.106 Å2 / Biso min: 15.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2388 Å / Luzzati sigma a obs: 0.192792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→41.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.169→2.226 Å / Total num. of bins used: 20
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