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Yorodumi- PDB-1ac5: CRYSTAL STRUCTURE OF KEX1(DELTA)P, A PROHORMONE-PROCESSING CARBOX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ac5 | |||||||||
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Title | CRYSTAL STRUCTURE OF KEX1(DELTA)P, A PROHORMONE-PROCESSING CARBOXYPEPTIDASE FROM SACCHAROMYCES CEREVISIAE | |||||||||
Components | KEX1(DELTA)P | |||||||||
Keywords | CARBOXYPEPTIDASE / HYDROLASE / GLYCOPROTEIN / TRANSMEMBRANE | |||||||||
Function / homology | Function and homology information carboxypeptidase D / serine-type carboxypeptidase activity / fungal-type vacuole / trans-Golgi network / apoptotic process / proteolysis / membrane Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / MIR, MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Shilton, B.H. / Thomas, D.Y. / Cygler, M. | |||||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Crystal structure of Kex1deltap, a prohormone-processing carboxypeptidase from Saccharomyces cerevisiae. Authors: Shilton, B.H. / Thomas, D.Y. / Cygler, M. #1: Journal: Eur.J.Biochem. / Year: 1994 Title: Secretion, Purification and Characterization of a Soluble Form of the Yeast Kex1-Encoded Protein from Insect-Cell Cultures Authors: Latchinian-Sadek, L. / Thomas, D.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ac5.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ac5.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ac5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ac5_validation.pdf.gz | 725.7 KB | Display | wwPDB validaton report |
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Full document | 1ac5_full_validation.pdf.gz | 731.8 KB | Display | |
Data in XML | 1ac5_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1ac5_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/1ac5 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/1ac5 | HTTPS FTP |
-Related structure data
Related structure data | 3sc2S 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: 54272.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09620, carboxypeptidase D |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 17% PEG-MME 5000, 400 MM AMMONIUM ACETATE, 5% GLYCEROL, 10 MM SODIUM AZIDE, PH 6.5. | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: used to seeding, Shilton, B.H., (1996) Protein Sci., 5, 395. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 20693 / % possible obs: 96.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 6 / % possible all: 90 |
Reflection | *PLUS % possible obs: 91.9 % / Redundancy: 5.11 % |
Reflection shell | *PLUS % possible obs: 81.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR, MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SC2 Resolution: 2.4→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: X-PLOR BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 21.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.44 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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