[English] 日本語
Yorodumi- PDB-6a6f: Crystal structure of Putative iron-sulfur cluster assembly scaffo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a6f | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Putative iron-sulfur cluster assembly scaffold protein for SUF system (FiSufU) from thermophilic Fervidobacterium Islandicum AW-1 | |||||||||
Components | Iron-sulfur cluster assembly scaffold protein NifU | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / SufE / Thermophile / Fe-S cluster scaffold protein | |||||||||
Function / homology | Function and homology information iron-sulfur cluster assembly / iron-sulfur cluster binding / iron ion binding Similarity search - Function | |||||||||
Biological species | Fervidobacterium islandicum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Dhanasingh, I. / Jin, H.S. / Lee, D.W. / Lee, S.H. | |||||||||
Funding support | Korea, Republic Of, 2items
| |||||||||
Citation | Journal: Microb Biotechnol / Year: 2020 Title: The sulfur formation system mediating extracellular cysteine-cystine recycling in Fervidobacterium islandicum AW-1 is associated with keratin degradation. Authors: Jin, H.S. / Dhanasingh, I. / Sung, J.Y. / La, J.W. / Lee, Y. / Lee, E.M. / Kang, Y. / Lee, D.Y. / Lee, S.H. / Lee, D.W. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6a6f.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6a6f.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 6a6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/6a6f ftp://data.pdbj.org/pub/pdb/validation_reports/a6/6a6f | HTTPS FTP |
---|
-Related structure data
Related structure data | 6a6eC 6a6gC 2qq4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15855.393 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Gene: NA23_08310 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1B0VLW5 |
---|
-Non-polymers , 5 types, 261 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PEG / #4: Chemical | #5: Chemical | ChemComp-NI / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.12 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.01M Nickel Chloride, PEG MEM 2000, 0.1M Tris HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 18186 / % possible obs: 98.74 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.0471 / Net I/σ(I): 24.96 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.092 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QQ4 Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.632 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.458 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|