[English] 日本語
![](img/lk-miru.gif)
- PDB-4q98: Crystal structure of a fimbrilin (fimA) from Porphyromonas gingiv... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4q98 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a fimbrilin (fimA) from Porphyromonas gingivalis W83 at 1.30 A resolution (PSI Community Target, Nakayama) | ||||||
![]() | Major fimbrial subunit protein | ||||||
![]() | CELL ADHESION / PF06321 / Type IV / PF15495 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | ![]() pilus / : / cell outer membrane / cell adhesion / structural molecule activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: A Distinct Type of Pilus from the Human Microbiome. Authors: Xu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Deacon, A.M. / Godzik, A. / ...Authors: Xu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Curtis, M.A. / Nakayama, K. / Wilson, I.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 180.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 145.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 412.2 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3liuC ![]() 3payC ![]() 3r4rC ![]() 3sy6C ![]() 3t2lC ![]() 3ufiC ![]() 3up6C ![]() 4dguC ![]() 4epsC ![]() 4gpvC ![]() 4h40C ![]() 4jg5C ![]() 4jrfC ![]() 4k4kC ![]() 4qb7C ![]() 4qdgC ![]() 4rdbC ![]() 5cagC C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-
Components
#1: Protein | Mass: 39319.156 Da / Num. of mol.: 1 / Fragment: UNP residues 3-373 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30.00% polyethylene glycol 6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2014 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→47.082 Å / Num. obs: 73835 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.99 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 15.19 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. A SODIUM ION (NA) MODELED WAS PRESENT IN CRYSTALLIZATION CONDITIONS. 4. THE DENSITIES FOR LOOP REGION (45-49) ARE POOR.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.39 Å2 / Biso mean: 19.0056 Å2 / Biso min: 7.26 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→47.082 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
|