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Yorodumi- PDB-3zod: Crystal structure of FMN-binding protein (NP_142786.1) from Pyroc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zod | ||||||
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Title | Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii with bound benzene-1,4-diol | ||||||
Components | FMN-BINDING PROTEIN | ||||||
Keywords | FMN-BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PYROCOCCUS HORIKOSHII (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 | 3zod.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zod.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zod ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zod | HTTPS FTP |
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-Related structure data
Related structure data | 3zocC 3zoeC 3zofC 3zogC 3zohC 2r6vS 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
#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-HQE / |
#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: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
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: 1.68→40 Å / Num. obs: 18582 / % possible obs: 89.2 % / Observed criterion σ(I): 3.5 / Redundancy: 11.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.68→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.7 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R6V Resolution: 1.68→39.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.828 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.134 / 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: 23.903 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→39.74 Å
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Refine LS restraints |
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