+Open data
-Basic information
Entry | Database: PDB / ID: 4fln | ||||||
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Title | Crystal structure of plant protease Deg2 | ||||||
Components |
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Keywords | HYDROLASE / protease / Deg / PDZ | ||||||
Function / homology | Function and homology information photosystem II repair / chloroplast stromal thylakoid / chloroplast organization / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / chloroplast / protein catabolic process / serine-type endopeptidase activity ...photosystem II repair / chloroplast stromal thylakoid / chloroplast organization / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / chloroplast / protein catabolic process / serine-type endopeptidase activity / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Gong, W. / Liu, L. / Sun, R. / Gao, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal structure of Arabidopsis deg2 protein reveals an internal PDZ ligand locking the hexameric resting state. Authors: Sun, R. / Fan, H. / Gao, F. / Lin, Y. / Zhang, L. / Gong, W. / Liu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fln.cif.gz | 550.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fln.ent.gz | 453.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/4fln ftp://data.pdbj.org/pub/pdb/validation_reports/fl/4fln | HTTPS FTP |
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-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
#1: Protein | Mass: 59598.277 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DEGP2, At2g47940, F17A22.33, T9J23.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O82261, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Protein/peptide | Mass: 459.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) #3: Protein/peptide | | Mass: 1851.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) #4: Water | ChemComp-HOH / | Sequence details | PROTEIN CHAINS D, E AND F IN THE STRUCTURE ARE CO-PURIFIED AND CO-CRYSTALLIZED PEPTIDES, WHICH ARE ...PROTEIN CHAINS D, E AND F IN THE STRUCTURE ARE CO-PURIFIED AND CO-CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 48456 / % possible obs: 98.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.104 / Rsym value: 0.107 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.385 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→29.742 Å / SU ML: 0.8 / σ(F): 1.34 / Phase error: 28.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.376 Å2 / ksol: 0.307 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.742 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.9814 Å / Origin y: 32.083 Å / Origin z: 35.0848 Å
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Refinement TLS group | Selection details: all |