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- PDB-3zog: Crystal structure of FMN-binding protein (NP_142786.1) from Pyroc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zog | ||||||
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Title | Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii with bound 1-Cyclohex-2-enone | ||||||
![]() | FMN-BINDING PROTEIN | ||||||
![]() | OXIDOREDUCTASE / ELECTRON TRANSPORT | ||||||
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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.9 KB | Display | ![]() |
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PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zocC ![]() 3zodC ![]() 3zoeC ![]() 3zofC ![]() 3zohC ![]() 1uscS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 21691.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-A2Q / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % / Description: NONE |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Feb 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0044 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45 Å / Num. obs: 18259 / % possible obs: 100 % / Observed criterion σ(I): 3.5 / Redundancy: 15.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1USC Resolution: 1.75→44.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.789 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 30.728 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→44.77 Å
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Refine LS restraints |
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