[English] 日本語
Yorodumi- PDB-5nzx: Crystal structure of DNA cross-link repair protein 1A in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nzx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of DNA cross-link repair protein 1A in complex with Ceftriaxone (alternative site) | ||||||
Components | DNA cross-link repair 1A protein | ||||||
Keywords | HYDROLASE / exonulcease / cephalosporin / cross-link repair / DCLRE1A | ||||||
Function / homology | Function and homology information 5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / fibrillar center / beta-lactamase activity / double-strand break repair via nonhomologous end joining / beta-lactamase / damaged DNA binding / cell cycle / cell division ...5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / fibrillar center / beta-lactamase activity / double-strand break repair via nonhomologous end joining / beta-lactamase / damaged DNA binding / cell cycle / cell division / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Newman, J.A. / Aitkenhead, H. / Kupinska, K. / Burgess-Brown, N.A. / Talon, R. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of DNA cross-link repair protein 1A in complex with Ceftriaxone (alternative site) Authors: Newman, J.A. / Aitkenhead, H. / Kupinska, K. / Burgess-Brown, N.A. / Talon, R. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5nzx.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5nzx.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 5nzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/5nzx ftp://data.pdbj.org/pub/pdb/validation_reports/nz/5nzx | HTTPS FTP |
---|
-Related structure data
Related structure data | 5ahoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38922.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1A, KIAA0086, SNM1, SNM1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PJP8 |
---|---|
#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-9F2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.02 % |
---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 30 % PEG 1000, 0.1 M MIB buffer pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→51.43 Å / Num. obs: 61686 / % possible obs: 97.5 % / Redundancy: 5.8 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.023 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.42→1.46 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3618 / CC1/2: 0.512 / Rpim(I) all: 0.787 / % possible all: 78.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5aho Resolution: 1.47→46.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.165 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 27.61 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.47→46.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|