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Yorodumi- PDB-2fge: Crystal structure of presequence protease PreP from Arabidopsis t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fge | ||||||
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Title | Crystal structure of presequence protease PreP from Arabidopsis thaliana | ||||||
Components |
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Keywords | HYDROLASE / PLANT PROTEIN / PEPTIDASOME / PROTEASE-PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information apoplast / chloroplast envelope / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / chloroplast stroma / response to cadmium ion / chloroplast / protein processing / metalloendopeptidase activity / mitochondrial matrix / mitochondrion ...apoplast / chloroplast envelope / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / chloroplast stroma / response to cadmium ion / chloroplast / protein processing / metalloendopeptidase activity / mitochondrial matrix / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Eneqvist, T. / Johnson, K.A. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: The closed structure of presequence protease PreP forms a unique 10 000 A(3) chamber for proteolysis Authors: Johnson, K.A. / Bhushan, S. / Hallberg, B.M. / Frohn, A. / Glaser, E. / Eneqvist, T. #1: Journal: Plant J. / Year: 2003 Title: Characterization of a novel zinc metalloprotease involved in degrading targeting peptides in mitochondria and chloroplasts Authors: Moberg, P. / Stahl, A. / Bhushan, S. / Wright, S.J. / Eriksson, A. / Bruce, B.D. / Glaser, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fge.cif.gz | 407.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fge.ent.gz | 342.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/2fge ftp://data.pdbj.org/pub/pdb/validation_reports/fg/2fge | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is a monomer |
-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABDE
#1: Protein | Mass: 112536.352 Da / Num. of mol.: 2 / Mutation: E80Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX-6P-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LJL3 #2: Protein/peptide | Mass: 602.704 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 956 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / #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: 2.28 Å3/Da / Density % sol: 46.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22% PEG 6000, 0.1M Hepes, 0.025M magnesium chloride, 0.1% beta-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-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 4 / Detector: CCD / Date: Nov 6, 2004 / Details: Khozu monochromator and toroidal Zeiss mirror |
Radiation | Monochromator: transparent diamond monochromators / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→93.66 Å / Num. all: 121080 / Num. obs: 116872 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.26 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→93.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.739 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.443 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→93.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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