[English] 日本語
Yorodumi- PDB-6frn: Structure of F420H2 oxidase (FprA) co-crystallized with 10mM Tb-X... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6frn | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of F420H2 oxidase (FprA) co-crystallized with 10mM Tb-Xo4 and calcium chloride | ||||||
Components | F420H2 oxidase (FprA) | ||||||
Keywords | OXIDOREDUCTASE / protein nucleation / phasing / Tb-Xo4 / crystallophore | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanothermococcus thermolithotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å | ||||||
Authors | Engilberge, S. / Riobe, F. / Di Pietro, S. / Wagner, T. / Shima, S. / Girard, E. / Dumont, E. / Maury, O. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: Chemistry / Year: 2018 Title: Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography. Authors: Engilberge, S. / Riobe, F. / Wagner, T. / Di Pietro, S. / Breyton, C. / Franzetti, B. / Shima, S. / Girard, E. / Dumont, E. / Maury, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6frn.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6frn.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6frn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/6frn ftp://data.pdbj.org/pub/pdb/validation_reports/fr/6frn | HTTPS FTP |
---|
-Related structure data
Related structure data | 6f2fC 6f2hC 6f2iC 6f2jC 6f2kC 6f2mC 6frmC 6froC 6frqC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 46242.230 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Methanothermococcus thermolithotrophicus (archaea) References: UniProt: A0A452CSW8*PLUS |
---|
-Non-polymers , 8 types, 946 molecules
#2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-TB / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PE4 / #7: Chemical | ChemComp-7MT / #8: Chemical | ChemComp-NA / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 28% PEG 400 and 200 mM calcium chloride in 100 mM Hepes pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97662 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97662 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→42.83 Å / Num. obs: 156147 / % possible obs: 98.92 % / Redundancy: 5.5 % / Biso Wilson estimate: 29.92 Å2 / Rpim(I) all: 0.04 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.74→1.84 Å / Rpim(I) all: 0.458 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.74→25.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.099
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.07 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.21 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.74→25.48 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.74→1.78 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|