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Yorodumi- PDB-4hcb: The metal-free form of crystal structure of E.coli ExoI-ssDNA complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hcb | ||||||
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Title | The metal-free form of crystal structure of E.coli ExoI-ssDNA complex | ||||||
Components |
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Keywords | HYDROLASE/DNA / DnaQ family / Exonuclease C-terminal family / 3'-5' exonuclease / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / 5'-deoxyribose-5-phosphate lyase activity / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / DNA repair / magnesium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Qiu, R. / Wei, J. / Lou, T. / Liu, M. / Ji, C. / Gong, W. | ||||||
Citation | Journal: To be published Title: The structures of Escherichia coli exonuclease I in complex with the single strand DNA Authors: Qiu, R. / Lou, T. / Wei, J. / Liu, M. / Gu, S. / Tang, R. / Ji, C. / Gong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hcb.cif.gz | 222 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hcb.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/4hcb ftp://data.pdbj.org/pub/pdb/validation_reports/hc/4hcb | HTTPS FTP |
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-Related structure data
Related structure data | 4hccC 3c95S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55381.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5alpha / Gene: b2011, cpeA, JW1993, sbcB, xonA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04995, exodeoxyribonuclease I #2: DNA chain | Mass: 3713.524 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The ssDNA samples were synthesized with 3'-phosphoryl modification (PAGE purified) #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Sequence details | THIS RESIDUE IS ASP FOR E.COLI STRAIN DH5ALPHA | |
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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: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.65-1.68 M ammonium sulfate, 6.5-6.8% v/v 2-propanol, 0.1 M sodium citrate tribasic dihydrate pH 6.0 and 5 mM phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.072 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. all: 72101 / Num. obs: 71457 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.083 / Χ2: 1.312 / Net I/σ(I): 14.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3C95 Resolution: 2→37.663 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8556 / SU ML: 0.5 / σ(F): 1.34 / Phase error: 21.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.013 Å2 / ksol: 0.363 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.59 Å2 / Biso mean: 32.88 Å2 / Biso min: 13 Å2
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Refinement step | Cycle: LAST / Resolution: 2→37.663 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26
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