+Open data
-Basic information
Entry | Database: PDB / ID: 3qo6 | ||||||
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Title | Crystal structure analysis of the plant protease Deg1 | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / protease / HtrA / pH-sensor / hydrolase | ||||||
Function / homology | Function and homology information photosystem II repair / thylakoid lumen / chloroplast thylakoid / thylakoid / chloroplast thylakoid membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / chloroplast / protein catabolic process / serine-type endopeptidase activity ...photosystem II repair / thylakoid lumen / chloroplast thylakoid / thylakoid / chloroplast thylakoid membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / chloroplast / protein catabolic process / serine-type endopeptidase activity / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Clausen, T. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: Structural adaptation of the plant protease Deg1 to repair photosystem II during light exposure. Authors: Kley, J. / Schmidt, B. / Boyanov, B. / Stolt-Bergner, P.C. / Kirk, R. / Ehrmann, M. / Knopf, R.R. / Naveh, L. / Adam, Z. / Clausen, T. | ||||||
History |
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Remark 999 | AUTHOR STATES THAT THE PEPTIDES WERE CO-PURIFIED AND CO-CRYSTALLIZED WITH THE DEG1 PROTEIN FROM E. ...AUTHOR STATES THAT THE PEPTIDES WERE CO-PURIFIED AND CO-CRYSTALLIZED WITH THE DEG1 PROTEIN FROM E.COLI, HOWEVER THEIR PRECISE ORIGIN IS UNKNOWN. THEY ARE MODELED AS ALA IN THE DEPOSITED PDB FILE AND HAVE BEEN CHANGED TO UNK DURING PROCESSING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qo6.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qo6.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 3qo6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qo6_validation.pdf.gz | 468.1 KB | Display | wwPDB validaton report |
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Full document | 3qo6_full_validation.pdf.gz | 510.7 KB | Display | |
Data in XML | 3qo6_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 3qo6_validation.cif.gz | 57.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/3qo6 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/3qo6 | HTTPS FTP |
-Related structure data
Related structure data | 3mh7S 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
-Protein/peptide , 4 types, 6 molecules DEHIFG
#2: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) | ||||
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#3: Protein/peptide | Mass: 358.434 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) #4: Protein/peptide | | Mass: 443.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) #5: Protein/peptide | | Mass: 273.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) |
-Protein / Non-polymers , 2 types, 141 molecules ABC
#1: Protein | Mass: 36785.508 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g27925, Deg1, DEGP, DEGP1, K16N12.18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O22609, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #6: Water | ChemComp-HOH / | |
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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: 3.52 Å3/Da / Density % sol: 65.07 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 5.2 Details: sodium citrate, ammonium sulfate, lithium sulfate, pH 5.2, vapor diffusion, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→20 Å / Num. all: 57809 / Num. obs: 53034 / % possible obs: 98.1 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -1000 / Rmerge(I) obs: 0.054 / Χ2: 1.083 / Net I/σ(I): 10.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MH7 Resolution: 2.5→15 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 75.6883 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.97 Å2 / Biso mean: 85.1888 Å2 / Biso min: 34.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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Xplor file |
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