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Yorodumi- PDB-7a6p: Structural determinants underlying the adduct lifetime in a short... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a6p | ||||||
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Title | Structural determinants underlying the adduct lifetime in a short LOV protein PpSB2-LOV | ||||||
Components | Putative Sensory box protein | ||||||
Keywords | SIGNALING PROTEIN / LOV domain / PAS domain / Dimerization / Signaling blue light photoreceptor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Arinkin, V. / Granzin, J. / Batra-Safferling, R. | ||||||
Citation | Journal: Febs J. / Year: 2021 Title: Structural determinants underlying the adduct lifetime in the LOV proteins of Pseudomonas putida. Authors: Arinkin, V. / Granzin, J. / 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 | 7a6p.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a6p.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 7a6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a6p_validation.pdf.gz | 481.6 KB | Display | wwPDB validaton report |
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Full document | 7a6p_full_validation.pdf.gz | 484.2 KB | Display | |
Data in XML | 7a6p_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 7a6p_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/7a6p ftp://data.pdbj.org/pub/pdb/validation_reports/a6/7a6p | HTTPS FTP |
-Related structure data
Related structure data | 3sw1S 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: 19210.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria) Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: PP_2739 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88JB0 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.23 Å3/Da / Density % sol: 44.6 % / Description: needle |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: Sodium acetate, polyethylene glycol 200, polyethylene glycol 3350 PH range: 4.9 - 5.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Mar 8, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.93→44.88 Å / Num. obs: 25353 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.053 / Rrim(I) all: 0.111 / Net I/σ(I): 8.9 / Num. measured all: 107111 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SW1 Resolution: 1.93→44.88 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 39.18 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→44.88 Å
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Refine LS restraints |
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