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Yorodumi- PDB-1nfp: STRUCTURAL REFINEMENT OF THE NON-FLUORESCENT FLAVOPROTEIN FROM PH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nfp | ||||||
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Title | STRUCTURAL REFINEMENT OF THE NON-FLUORESCENT FLAVOPROTEIN FROM PHOTOBACTERIUM LEIOGNATHI AT 1.60 ANGSTROMS RESOLUTION | ||||||
Components | LUXF GENE PRODUCT | ||||||
Keywords | FLAVOPROTEIN / FLAVIN MONONUCLEOTIDE / MYRISTATE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Photobacterium leiognathi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Moore, S.A. / Njames, M.N.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.60 A resolution. Authors: Moore, S.A. / James, M.N. #1: Journal: Protein Sci. / Year: 1994 Title: Common Structural Features of the Luxf Protein and the Subunits of Bacterial Luciferase: Evidence for a (Beta(Slash)Alpha)8 Fold in Luciferase Authors: Moore, S.A. / James, M.N.G. #2: Journal: Embo J. / Year: 1993 Title: Crystal Structure of a Flavoprotein Related to the Subunits of Bacterial Luciferase Authors: Moore, S.A. / James, M.N.G. / O'Kane, D.J. / Lee, J. #3: Journal: J.Mol.Biol. / Year: 1992 Title: Crystallization of Photobacterium Leiognathi Nfp, Non-Fluorescent Flavoprotein an Unusual Flavoprotein with Limited Sequence Identity to Bacterial Luciferase Authors: Moore, S.A. / James, M.N.G. / O'Kane, D.J. / Lee, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nfp.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nfp.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 1nfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nfp_validation.pdf.gz | 534.5 KB | Display | wwPDB validaton report |
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Full document | 1nfp_full_validation.pdf.gz | 544.2 KB | Display | |
Data in XML | 1nfp_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1nfp_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nfp ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nfp | HTTPS FTP |
-Related structure data
Similar structure data |
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-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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Details | SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 1 1 .. 423 TWO-FOLD AXIS AT 0,Y,1/4: THE MOLECULE IS A SYMMETRICAL HOMODIMER. SYMMETRY1 1 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 49.66500 |
-Components
#1: Protein | Mass: 26312.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photobacterium leiognathi (bacteria) / References: UniProt: P09142 | ||||||
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#2: Chemical | ChemComp-SO4 / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | THE STRUCTURAL FORMULA HYDROGEN ATOMS EQUIVALENTS PERTAIN TO THE OXIDIZED STATE OF FMN. THE ...THE STRUCTURAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % / Description: DATA COLLECTED FROM TWO CRYSTALS | |||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 51 % | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
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Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 1, 1992 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Num. obs: 28223 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.059 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 9999 Å / Num. measured all: 84138 / Rmerge(I) obs: 0.059 / Biso Wilson estimate: 16.07 Å2 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.67 Å / % possible obs: 65.6 % / Num. unique obs: 2590 / Num. measured obs: 3954 |
-Processing
Software |
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Refinement | Resolution: 1.6→10 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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