[English] 日本語
![](img/lk-miru.gif)
- PDB-2pil: Crystallographic Structure of Phosphorylated Pilin from Neisseria... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2pil | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystallographic Structure of Phosphorylated Pilin from Neisseria: Phosphoserine Sites Modify Type IV Pilus Surface Chemistry | |||||||||
![]() | TYPE 4 PILIN | |||||||||
![]() | CELL ADHESION / TYPE IV PILIN / FIBER-FORMING PROTEIN / MEMBRANE PROTEIN / DNA INDING PROTEIN / CONTRACTILE PROTEIN | |||||||||
Function / homology | ![]() protein secretion by the type II secretion system / type II protein secretion system complex / pilus / cell adhesion / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Forest, K.T. / Dunham, S.A. / Koomey, M. / Tainer, J.A. | |||||||||
![]() | ![]() Title: Crystallographic structure reveals phosphorylated pilin from Neisseria: phosphoserine sites modify type IV pilus surface chemistry and fibre morphology. Authors: Forest, K.T. / Dunham, S.A. / Koomey, M. / Tainer, J.A. #1: ![]() Title: Structure of the Fibre-Forming Protein Pilin at 2.6 A Resolution Authors: Parge, H.E. / Forest, K.T. / Hickey, M.J. / Christensen, D.A. / Getzoff, E.D. / Tainer, J.A. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 46.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 17286.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: Polysaccharide | alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-PT / |
#4: Chemical | ChemComp-HTO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8 Details: PROTEIN WAS CRYSTALLIZED FROM 60% PEG400, 50 MM CHESS, PH 8.0, 1% BETA-OCTYL GLUCOSIDE, 0.6% 1,2,3-HEPTANETRIOL. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1993 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→24 Å / Num. obs: 6565 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.081 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.6→2.78 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.307 / % possible all: 80.2 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: FITTING BEGAN WITH PDB MODEL 1AY2. PHOSPHOSERINE 68 WAS ADDED AND A BULK SOLVENT CORRECTION WAS APPLIED. THE EXPECTED N-TERMINAL METHYL-PHE WAS VERIFIED BY N-TERMINAL SEQUENCING BUT WAS NOT ...Details: FITTING BEGAN WITH PDB MODEL 1AY2. PHOSPHOSERINE 68 WAS ADDED AND A BULK SOLVENT CORRECTION WAS APPLIED. THE EXPECTED N-TERMINAL METHYL-PHE WAS VERIFIED BY N-TERMINAL SEQUENCING BUT WAS NOT INCLUDED IN THE MODEL BECAUSE IT IS NOT APPARENT IN ELECTRON DENSITY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.312 |