+Open data
-Basic information
Entry | Database: PDB / ID: 5luv | ||||||
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Title | Short LOV protein W619_1 in apo-state | ||||||
Components | Putative PAS/PAC sensor protein | ||||||
Keywords | SIGNALING PROTEIN / LOV domain / PAS domain / apo-state | ||||||
Function / homology | Function and homology information PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain ...PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Arinkin, V. / Granzin, J. / Batra-Safferling, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: Structure of a LOV protein in apo-state and implications for construction of LOV-based optical tools. Authors: Arinkin, V. / Granzin, J. / Rollen, K. / Krauss, U. / Jaeger, K.E. / Willbold, D. / Batra-Safferling, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5luv.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5luv.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 5luv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5luv_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 5luv_full_validation.pdf.gz | 454.2 KB | Display | |
Data in XML | 5luv_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 5luv_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/5luv ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5luv | HTTPS FTP |
-Related structure data
Related structure data | 5j3wS 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: 19115.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: W619 / Gene: PputW619_0812 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1J385 #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: 3.74 Å3/Da / Density % sol: 67.07 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / Details: 1M NH4SO4, 0.1M MES / PH range: 6.0 - 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2014 |
Radiation | Monochromator: Silicon (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.6 Å / Num. obs: 19498 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rsym value: 0.111 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.908 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.336 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J3W Resolution: 2.5→43.559 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→43.559 Å
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Refine LS restraints |
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LS refinement shell |
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