[English] 日本語
Yorodumi- PDB-2nq9: High resolution crystal structure of Escherichia coli endonucleas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nq9 | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) Y72A mutant bound to damaged DNA | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / TIM-barrel / trinuclear Zn active site / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding ...deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Garcin-Hosfield, E.D. / Hosfield, D.J. / Tainer, J.A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Authors: Garcin, E.D. / Hosfield, D.J. / Desai, S.A. / Haas, B.J. / Bjoras, M. / Cunningham, R.P. / Tainer, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2nq9.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2nq9.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 2nq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nq9_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2nq9_full_validation.pdf.gz | 449.7 KB | Display | |
Data in XML | 2nq9_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 2nq9_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/2nq9 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/2nq9 | HTTPS FTP |
-Related structure data
Related structure data | 2nqhC 2nqjC 1qtwS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-DNA chain , 3 types, 3 molecules BCD
#1: DNA chain | Mass: 1783.216 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: DNA chain | Mass: 1394.951 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 3372.234 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 31426.402 Da / Num. of mol.: 1 / Mutation: Y72A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nfo / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): nfo- strain BW565DE3 / References: UniProt: P0A6C1, deoxyribonuclease IV |
---|
-Non-polymers , 2 types, 349 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.05 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% MPEG-2000, 0.1 M HEPES pH 7, and 0.4 M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→20 Å / Num. obs: 78368 / % possible obs: 98 % / Observed criterion σ(I): 278343 / Rsym value: 0.098 / Net I/σ(I): 18.3 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1QTW Resolution: 1.45→20 Å / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.63 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.54 Å / Rfactor Rfree error: 0.01
|