+Open data
-Basic information
Entry | Database: PDB / ID: 5djt | ||||||
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Title | Crystal structure of LOV2 (C450A) domain in complex with Zdk2 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Protein binding / Protein engineering / Photoswitch / Light-induced signal transduction / LOV2 / Affibody / Complex | ||||||
Function / homology | Function and homology information blue light photoreceptor activity / protein kinase activity / protein phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Avena sativa (oats) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Tarnawski, M. / Wang, H. / Yumerefendi, H. / Hahn, K.M. / Schlichting, I. | ||||||
Citation | Journal: Nat.Methods / Year: 2016 Title: LOVTRAP: an optogenetic system for photoinduced protein dissociation. Authors: Wang, H. / Vilela, M. / Winkler, A. / Tarnawski, M. / Schlichting, I. / Yumerefendi, H. / Kuhlman, B. / Liu, R. / Danuser, G. / Hahn, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5djt.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5djt.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 5djt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/5djt ftp://data.pdbj.org/pub/pdb/validation_reports/dj/5djt | HTTPS FTP |
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-Related structure data
Related structure data | 5djuC 5efwC 2kzjS 2wkqS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 16631.729 Da / Num. of mol.: 1 / Fragment: UNP residues 404-546 / Mutation: C450A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Avena sativa (oats) / Gene: NPH1-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O49004 |
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#2: Protein | Mass: 6674.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 4 types, 279 molecules
#3: Chemical | ChemComp-CU / |
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#4: Chemical | ChemComp-FMN / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M tri-sodium citrate pH 5.6, 0.2 M ammonium acetate, 32% (w/v) PEG 4000 and 0.1 M copper(II) chloride as an additive |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00005 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 44465 / % possible obs: 99.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WKQ and a homology model based on 2KZJ Resolution: 1.4→35.507 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 14.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→35.507 Å
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Refine LS restraints |
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LS refinement shell |
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