+Open data
-Basic information
Entry | Database: PDB / ID: 6non | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Cyanthece apo McdA | ||||||
Components | Cobyrinic acid ac-diamide synthase | ||||||
Keywords | DNA BINDING PROTEIN / nonspecific DNA binding protein / Walker box / ParA-like / Carboxysome / McdA / McdB | ||||||
Function / homology | AAA domain / AAA domain / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-DIPHOSPHATE / Maintenance of carboxysome distribution protein A Function and homology information | ||||||
Biological species | Cyanothece (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.68 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structures of maintenance of carboxysome distribution Walker-box McdA and McdB adaptor homologs. Authors: Schumacher, M.A. / Henderson, M. / Zhang, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6non.cif.gz | 203.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6non.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 6non.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/6non ftp://data.pdbj.org/pub/pdb/validation_reports/no/6non | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29325.689 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanothece (bacteria) / Gene: PCC7424_5529 / Production host: Escherichia coli (E. coli) / References: UniProt: B7KMS4 #2: Chemical | ChemComp-ADP / | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.39 Å3/Da / Density % sol: 77.17 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2018 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→134.5 Å / Num. obs: 61015 / % possible obs: 80.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 57.51 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.045 / Rsym value: 0.07 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.68→275 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.616 / Rpim(I) all: 0.47 / Rsym value: 0.567 |
-Phasing
Phasing | Method: MAD |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.68→77.676 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 23.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 30.912 Å2 / ksol: 0.318 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→77.676 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|