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Yorodumi- PDB-1jji: The Crystal Structure of a Hyper-thermophilic Carboxylesterase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jji | ||||||
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Title | The Crystal Structure of a Hyper-thermophilic Carboxylesterase from the Archaeon Archaeoglobus fulgidus | ||||||
Components | Carboxylesterase | ||||||
Keywords | HYDROLASE / alpha-beta hydrolase fold | ||||||
Function / homology | Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Carboxylesterase (EstA) Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | De Simone, G. / Menchise, V. / Manco, G. / Mandrich, L. / Sorrentino, N. / Lang, D. / Rossi, M. / Pedone, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The crystal structure of a hyper-thermophilic carboxylesterase from the archaeon Archaeoglobus fulgidus. Authors: De Simone, G. / Menchise, V. / Manco, G. / Mandrich, L. / Sorrentino, N. / Lang, D. / Rossi, M. / Pedone, C. #1: Journal: ARCH.BIOCHEM.BIOPHYS. / Year: 2000 Title: Cloning, Overexpression and Properties of a New Thermophilic and Termostable Esterase with Sequence Similarity to Hormone-Sensitive Lipase Subfamily from the archaeon Archaeoglobus fulgidus Authors: Manco, G. / Giosue, E. / D'Auria, S. / Herman, P. / Carrea, G. / Rossi, M. #2: Journal: J.Mol.Biol. / Year: 2000 Title: A snapshot of the transition state of a novel thermophilic esterase belonging to the subfamily of mammalian hormone-sensitive lipase Authors: De Simone, G. / Galdiero, S. / Manco, G. / Lang, D. / Rossi, M. / Pedone, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jji.cif.gz | 265.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jji.ent.gz | 215.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jji_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
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Full document | 1jji_full_validation.pdf.gz | 505.5 KB | Display | |
Data in XML | 1jji_validation.xml.gz | 55.4 KB | Display | |
Data in CIF | 1jji_validation.cif.gz | 77 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/1jji ftp://data.pdbj.org/pub/pdb/validation_reports/jj/1jji | HTTPS FTP |
-Related structure data
Related structure data | 1evqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35530.164 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: PT7-7SCII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28558, carboxylesterase #2: Chemical | ChemComp-EPE / #3: 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: 3.03 Å3/Da / Density % sol: 59.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Peg 4000, Magnesium acetate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 28, 2000 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 84834 / Num. obs: 84834 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.94 / % possible all: 98.5 |
Reflection | *PLUS Num. measured all: 920049 |
Reflection shell | *PLUS % possible obs: 84.7 % / Rmerge(I) obs: 0.361 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EVQ Resolution: 2.2→8 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.203 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |