[English] 日本語
Yorodumi- PDB-6aiq: High resolution structure of recombinant high-potential iron-sulf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aiq | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution structure of recombinant high-potential iron-sulfur protein | ||||||
Components | High-potential iron-sulfur protein | ||||||
Keywords | METAL BINDING PROTEIN / IRON-SULFUR PROTEIN / METAL-BINDING PROTEIN | ||||||
Function / homology | Function and homology information aerobic electron transport chain / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermochromatium tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å | ||||||
Authors | Hanazono, Y. / Takeda, K. / Miki, K. | ||||||
Citation | Journal: Proteins / Year: 2020 Title: Characterization of perdeuterated high-potential iron-sulfur protein with high-resolution X-ray crystallography. Authors: Hanazono, Y. / Takeda, K. / Miki, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6aiq.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6aiq.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 6aiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6aiq ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6aiq | HTTPS FTP |
---|
-Related structure data
Related structure data | 6airC 3a39S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8793.851 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochromatium tepidum (bacteria) / Gene: hip / Production host: Escherichia coli (E. coli) / References: UniProt: P80176 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SF4 / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.65 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 1.7 M ammonium sulfate, 0.1 M Na citrate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→50 Å / Num. obs: 56295 / % possible obs: 98.3 % / Redundancy: 6.2 % / Rsym value: 0.082 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 0.85→0.86 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5 / Rsym value: 0.188 / % possible all: 82.6 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A39 Resolution: 0.85→36.32 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→36.32 Å
|