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Yorodumi- PDB-5e3x: Crystal structure of thermostable Carboxypeptidase (FisCP) from F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e3x | ||||||
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Title | Crystal structure of thermostable Carboxypeptidase (FisCP) from Fervidobacterium Islandicum AW-1 | ||||||
Components | Thermostable carboxypeptidase 1 | ||||||
Keywords | HYDROLASE / Carboxypeptidase / Fervidobacterium / FisCP | ||||||
Function / homology | Function and homology information carboxypeptidase Taq / metallocarboxypeptidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Fervidobacterium islandicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å | ||||||
Authors | Dhanasingh, I. / Lee, Y.-J. / Lee, D.W. / Lee, S.H. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: Biochemical and structural characterization of a keratin-degrading M32 carboxypeptidase from Fervidobacterium islandicum AW-1 Authors: Lee, Y.-J. / Dhanasingh, I. / Ahn, J.-S. / Jin, H.-S. / Choi, J.M. / Lee, S.H. / Lee, D.-W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e3x.cif.gz | 120.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e3x.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 5e3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e3x_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 5e3x_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 5e3x_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5e3x_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/5e3x ftp://data.pdbj.org/pub/pdb/validation_reports/e3/5e3x | HTTPS FTP |
-Related structure data
Related structure data | 1wgz 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
#1: Protein | Mass: 57316.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Strain: AW-1 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A140UHP3*PLUS |
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#2: Chemical | ChemComp-CO / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE OF THE PROTEIN HAS BEEN DEPOSITED TO NCBI WITH ACCESSION NUMBER WP_033190981.1. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % / Description: Hexagonal planar |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10%PEG1000 10%PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 26, 2015 |
Radiation | Monochromator: DCM Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.197→50 Å / Num. obs: 28236 / % possible obs: 99.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.62 |
Reflection shell | Resolution: 2.197→2.275 Å / % possible all: 98.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WGZ 1wgz Resolution: 2.197→33.324 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.197→33.324 Å
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Refine LS restraints |
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LS refinement shell |
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