[English] 日本語
![](img/lk-miru.gif)
- PDB-5w30: Crystal structure of mutant CJ YCEI protein (CJ-N48C) with monobr... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5w30 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mutant CJ YCEI protein (CJ-N48C) with monobromobimane guest structure | ||||||
![]() | Putative periplasmic protein | ||||||
![]() | UNKNOWN FUNCTION / nanotechnology nanoporous | ||||||
Function / homology | ![]() Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, T.R. / Snow, C.D. | ||||||
![]() | ![]() Title: Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals. Authors: Huber, T.R. / McPherson, E.C. / Keating, C.E. / Snow, C.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 50.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 742.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 742.9 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w17C ![]() 5w2dC ![]() 5w2kC ![]() 5w2rC ![]() 5w2vC ![]() 5w2xSC ![]() 5w2zC ![]() 5w31C ![]() 5w32C ![]() 5w37C ![]() 5w39C ![]() 5w3aC ![]() 5w3bC ![]() 5w3cC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20188.832 Da / Num. of mol.: 1 / Mutation: N48C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700819 / NCTC 11168 / Gene: Cj0420 / Plasmid: pSB3 / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-UNL / Mass: 282.547 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Chemical | #4: Chemical | ChemComp-9UM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Mosaicity: 0.34 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3.2 M Ammonium Sulfate, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Apr 4, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→38.57 Å / Num. all: 13196 / Num. obs: 13196 / % possible obs: 100 % / Redundancy: 19.2 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.264 / Rsym value: 0.257 / Net I/av σ(I): 2.5 / Net I/σ(I): 11.4 / Num. measured all: 253774 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5W2X Resolution: 2.75→38.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.989 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.228 / Details: U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.63 Å2 / Biso mean: 79.369 Å2 / Biso min: 45.07 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→38.57 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|