+Open data
-Basic information
Entry | Database: PDB / ID: 4ic5 | ||||||
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Title | Crystal structure of Deg5 | ||||||
Components | Protease Do-like 5, chloroplastic | ||||||
Keywords | HYDROLASE / Bets-barrel / endopeptidase / Calcium Binding / chloroplast | ||||||
Function / homology | Function and homology information photosystem II repair / thylakoid lumen / chloroplast thylakoid lumen / thylakoid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / chloroplast / serine-type endopeptidase activity / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.607 Å | ||||||
Authors | Gong, W. / Sun, W. / Fan, H. / Gao, F. / Liu, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: The structures of Arabidopsis Deg5 and Deg8 reveal new insights into HtrA proteases Authors: Sun, W. / Gao, F. / Fan, H. / Shan, X. / Sun, R. / Liu, L. / Gong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ic5.cif.gz | 258.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ic5.ent.gz | 206.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ic5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/4ic5 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/4ic5 | HTTPS FTP |
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-Related structure data
Related structure data | 4ic6C 1l1jS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 31489.041 Da / Num. of mol.: 3 / Mutation: S217A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DEGP5, HHOA, At4g18370, F28J12.30 / Production host: Escherichia coli (E. coli) References: UniProt: Q9SEL7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Calcium chloride dihydrate, 0.1M Tris-HCl, 25%(v/v) PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 33072 / Num. obs: 33338 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.6→2.6 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L1J Resolution: 2.607→49.883 Å / SU ML: 0.74 / σ(F): 1.34 / Phase error: 24.42 / 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: 40.238 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.607→49.883 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: -17.221 Å / Origin y: 20.9944 Å / Origin z: -15.4047 Å
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Refinement TLS group | Selection details: all |