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- PDB-3zoh: Crystal structure of FMN-binding protein (YP_005476) from Thermus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zoh | ||||||
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Title | Crystal structure of FMN-binding protein (YP_005476) from Thermus thermophilus with bound 1-Cyclohex-2-enone | ||||||
![]() | FLAVOREDOXIN | ||||||
![]() | FMN-BINDING PROTEIN / CYCLOHEXENONE | ||||||
Function / homology | ![]() oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / FMN binding Similarity search - Function | ||||||
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 | ![]() | 170.6 KB | Display | ![]() |
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PDB format | ![]() | 136.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 37.3 KB | Display | |
Data in CIF | ![]() | 52.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zocC ![]() 3zodC ![]() 3zoeC ![]() 3zofC ![]() 3zogC ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19741.439 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-A2Q / #3: Chemical | ChemComp-FMN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Details: 12.5% PEG 1000, 12.5% W/V PEG 3350, 12.5% V/V MPD AND 0.1 M ACETATE BUFFER PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2011 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.65→30 Å / Num. obs: 86300 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5 | |||||||||||||||
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1USC Resolution: 1.65→29.53 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.396 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.019 / 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: 23.136 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→29.53 Å
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Refine LS restraints |
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