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Yorodumi- PDB-3zog: Crystal structure of FMN-binding protein (NP_142786.1) from Pyroc... -
+Open data
-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 | ||||||
Components | FMN-BINDING PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PYROCOCCUS HORIKOSHII (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Pavkov-Keller, T. / Steinkellner, G. / Gruber, C.C. / Steiner, K. / Winkler, C. / Schwamberger, O. / Schwab, H. / Faber, K. / Gruber, K. | ||||||
Citation | Journal: Nat.Commun. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zog.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zog.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zog_validation.pdf.gz | 770.2 KB | Display | wwPDB validaton report |
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Full document | 3zog_full_validation.pdf.gz | 771.8 KB | Display | |
Data in XML | 3zog_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 3zog_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zog ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zog | HTTPS FTP |
-Related structure data
Related structure data | 3zocC 3zodC 3zoeC 3zofC 3zohC 1uscS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) PYROCOCCUS HORIKOSHII (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O58586 |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-A2Q / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0044 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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