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Yorodumi- PDB-3gfy: Klebsiella pneumoniae BlrP1 with FMN and cyclic diGMP, no metal ions -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gfy | ||||||
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Title | Klebsiella pneumoniae BlrP1 with FMN and cyclic diGMP, no metal ions | ||||||
Components | Klebsiella pneumoniae BlrP1 | ||||||
Keywords | HYDROLASE / SIGNALING PROTEIN / TIM-barrel / EAL domain / BLUF domain | ||||||
Function / homology | Function and homology information blue light photoreceptor activity / FAD binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Barends, T. / Hartmann, E. / Griese, J. / Beitlich, T. / Kirienko, N. / Ryjenkov, D. / Reinstein, J. / Shoeman, R. / Gomelsky, M. / Schlichting, I. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Authors: Barends, T.R. / Hartmann, E. / Griese, J.J. / Beitlich, T. / Kirienko, N.V. / Ryjenkov, D.A. / Reinstein, J. / Shoeman, R.L. / Gomelsky, M. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gfy.cif.gz | 160.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gfy.ent.gz | 125.4 KB | Display | PDB format |
PDBx/mmJSON format | 3gfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/3gfy ftp://data.pdbj.org/pub/pdb/validation_reports/gf/3gfy | HTTPS FTP |
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-Related 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: 45934.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria) Gene: blrp1, KPN78578_15680, KPN_01598 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE-3) / References: UniProt: A6T8V8 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: protein in 5 mM cy-diGMP, 5 mM CaCl2, 25 mM Tris-HCl pH 8.0, 40 mM NaCl, 5 mM MgCl2, 2 mM EDTA, 2 mM DTE, 5% glycerol, reservoir 0.1 M Na-Ac buffer pH 4.5, 0.2 M Ca-acetate, 17-20%PEG 3350, ...Details: protein in 5 mM cy-diGMP, 5 mM CaCl2, 25 mM Tris-HCl pH 8.0, 40 mM NaCl, 5 mM MgCl2, 2 mM EDTA, 2 mM DTE, 5% glycerol, reservoir 0.1 M Na-Ac buffer pH 4.5, 0.2 M Ca-acetate, 17-20%PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98407 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2007 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98407 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.56 Å / Num. all: 25028 / Num. obs: 25028 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.352 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→46.56 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.846 / SU B: 12.779 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.979 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.859 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→46.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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