[English] 日本語
Yorodumi- PDB-5g3d: preserving Metallic Sites Affected by Radiation Damage the CuT2 c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g3d | ||||||
---|---|---|---|---|---|---|---|
Title | preserving Metallic Sites Affected by Radiation Damage the CuT2 cCase in Thermus Thermophilus Multicopper Oxidase | ||||||
Components | THERMUS THERMOPHILUS MULTICOPPER OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / MULTICOPPER OXIDASE / RADIATION DAMAGE / METALLIC SITES / MACROMOLECULAR CRYSTALLOGRAPHY / RADICAL SCAVENGERS | ||||||
Function / homology | Function and homology information hydroquinone:oxygen oxidoreductase activity / laccase / ferroxidase activity / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Ruiz-Arellano, R. / Diaz, A. / Rosas, E. / Rudino, E. | ||||||
Citation | Journal: To be Published Title: Preserving Metallic Sites Affected by Radiation Damage the Cut2 Case in Thermus Thermophilus Multicopper Oxidase Authors: Ruiz-Arellano, R. / Diaz, A. / Rosas, E. / Stojanoff, V. / Rudino, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5g3d.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5g3d.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 5g3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g3d ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g3d | HTTPS FTP |
---|
-Related structure data
Related structure data | 5g3bC 5g3cC 5g3eC 5g3fC 5g3gC 5g3hC 2yaeS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48791.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-462 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: I7AL37, UniProt: Q72HW2*PLUS, laccase |
---|
-Non-polymers , 5 types, 455 molecules
#2: Chemical | #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MRD / ( #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9793 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.72 Å / Num. obs: 54103 / % possible obs: 98.2 % / Observed criterion σ(I): 18.08 / Redundancy: 6.3 % / Biso Wilson estimate: 11.97 Å2 / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / % possible all: 97 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YAE Resolution: 1.78→19.7 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 15.79 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→19.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|