+Open data
-Basic information
Entry | Database: PDB / ID: 4ic6 | ||||||
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Title | Crystal structure of Deg8 | ||||||
Components | Protease Do-like 8, chloroplastic | ||||||
Keywords | HYDROLASE / Beta-barrel | ||||||
Function / homology | Function and homology information photosystem II repair / thylakoid lumen / chloroplast thylakoid / chloroplast thylakoid lumen / thylakoid / plastid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / chloroplast / peptidase activity / serine-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 4ic6.cif.gz | 382 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ic6.ent.gz | 314.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ic6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ic6_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 4ic6_full_validation.pdf.gz | 464 KB | Display | |
Data in XML | 4ic6_validation.xml.gz | 42 KB | Display | |
Data in CIF | 4ic6_validation.cif.gz | 60.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/4ic6 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/4ic6 | HTTPS FTP |
-Related structure data
Related structure data | 4ic5C 3rfd C: citing same article (ref.) 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: 38808.234 Da / Num. of mol.: 3 / Fragment: UNP residues 91-448 / Mutation: S204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DEGP8, At5g39830, K13H13.1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9LU10, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Water | ChemComp-HOH / | |
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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: 2.38 Å3/Da / Density % sol: 48.27 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M sodium citrate tribasic dihydrate, 16.25% PEG3350, 5% jeffamine M600, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 73969 / Num. obs: 73478 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RFD 3rfd Resolution: 2→29.591 Å / SU ML: 0.57 / σ(F): 1.33 / Phase error: 24.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.436 Å2 / ksol: 0.302 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→29.591 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: 26
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Refinement TLS params. | Method: refined / Origin x: 41.7058 Å / Origin y: -20.076 Å / Origin z: -51.8657 Å
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Refinement TLS group | Selection details: all |