+Open data
-Basic information
Entry | Database: PDB / ID: 6jcc | ||||||
---|---|---|---|---|---|---|---|
Title | structure of a de novo protein D_1CY5_M1 | ||||||
Components | Computational designed protein based on evolution | ||||||
Keywords | DE NOVO PROTEIN / designed protein evolution crystal structure helix | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Meng, W. / Feng, T. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: structure of a computationally designed mutant protein D_1CY5_M1 Authors: Meng, W. / Haiyan, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jcc.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jcc.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 6jcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/6jcc ftp://data.pdbj.org/pub/pdb/validation_reports/jc/6jcc | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11085.901 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.92 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 15784 / % possible obs: 98.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.023 / Rrim(I) all: 0.065 / Net I/av σ(I): 4.588 / Net I/σ(I): 29.37 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.422 / Num. unique obs: 1523 / Rpim(I) all: 0.159 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.45→32.8 Å / Cross valid method: THROUGHOUT
| ||||||||||||||||||||
Solvent computation | Bsol: 47.2 Å2 / ksol: 0.46 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 16.63 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→32.8 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.451→1.489 Å
|