[English] 日本語
![](img/lk-miru.gif)
- PDB-3zoc: Crystal structure of FMN-binding protein (NP_142786.1) from Pyroc... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3zoc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii with bound p-hydroxybenzaldehyde | ||||||
![]() | FMN-BINDING PROTEIN | ||||||
![]() | FMN-BINDING PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pavkov-Keller, T. / Steinkellner, G. / Gruber, C.C. / Steiner, K. / Winkler, C. / Schwamberger, O. / Schwab, H. / Faber, K. / Gruber, K. | ||||||
![]() | ![]() Title: Identification of Promiscuous Ene-Reductase Activity by Mining Structural Databases Using Active Site Constellations. Authors: Steinkellner, G. / Gruber, C.C. / Pavkov-Keller, T. / Binter, A. / Steiner, K. / Winkler, C. / Lyskowski, A. / Schwamberger, O. / Oberer, M. / Schwab, H. / Faber, K. / Macheroux, P. / Gruber, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 51.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 35 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3zodC ![]() 3zoeC ![]() 3zofC ![]() 3zogC ![]() 3zohC ![]() 2r6vS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21691.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-HBA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: VAPOR DIFFUSION AT 293K; CONDITIONS CONTAINING PEG 3350 OR 6000 (10-20% W/V) AS PRECIPITATION AGENT AND DIFFERENT SALTS (50-200 MM MAGNESIUM CLORIDE, POTASSIUM FORMATE, NATRIUM FORMATE, ...Details: VAPOR DIFFUSION AT 293K; CONDITIONS CONTAINING PEG 3350 OR 6000 (10-20% W/V) AS PRECIPITATION AGENT AND DIFFERENT SALTS (50-200 MM MAGNESIUM CLORIDE, POTASSIUM FORMATE, NATRIUM FORMATE, AMMONIUM FORMATE, MAGNESIUM FORMATE) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Apr 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 9300 / % possible obs: 85.1 % / Observed criterion σ(I): 4 / Redundancy: 7.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.3 / % possible all: 90 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2R6V Resolution: 2.1→19.57 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.731 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.423 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY FEW RESIDUES FROM THE HIS-TAG AND LINKER REGIONS CAN BE RESOLVED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 25.634 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|