[English] 日本語
Yorodumi- PDB-4hcc: The zinc ion bound form of crystal structure of E.coli ExoI-ssDNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hcc | ||||||
---|---|---|---|---|---|---|---|
Title | The zinc ion bound form of crystal structure of E.coli ExoI-ssDNA complex | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / DnaQ family / Exonuclease C-terminal family / 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: 2.96 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hcc.cif.gz | 210.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hcc.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hcc_validation.pdf.gz | 486.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4hcc_full_validation.pdf.gz | 495 KB | Display | |
Data in XML | 4hcc_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 4hcc_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/4hcc ftp://data.pdbj.org/pub/pdb/validation_reports/hc/4hcc | HTTPS FTP |
-Related structure data
Related structure data | 4hcbSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein / DNA chain , 2 types, 4 molecules ABCD
#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) |
---|
-Non-polymers , 5 types, 34 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | THIS RESIDUE IS ASP FOR E.COLI STRAIN DH5ALPHA |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.42 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: The crystals grew in 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, 5 mM phenol, then soaked in the solution consisted of precipitant ...Details: The crystals grew in 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, 5 mM phenol, then soaked in the solution consisted of precipitant solution and 20 mM zinc chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→30 Å / Num. all: 23347 / Num. obs: 23141 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.091 / Χ2: 1.189 / Net I/σ(I): 12.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4HCB Resolution: 2.96→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0 / SU B: 16.616 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
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: 131.34 Å2 / Biso mean: 62.8263 Å2 / Biso min: 27.78 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.96→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.96→3.035 Å / Total num. of bins used: 20
|