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Yorodumi- PDB-3sc2: REFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sc2 | ||||||||||||
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Title | REFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-ANGSTROMS RESOLUTION | ||||||||||||
Components | (SERINE CARBOXYPEPTIDASE II (CPDW-II)) x 2 | ||||||||||||
Keywords | HYDROLASE(CARBOXYPEPTIDASE) | ||||||||||||
Function / homology | Function and homology information carboxypeptidase D / serine-type carboxypeptidase activity / proteolysis Similarity search - Function | ||||||||||||
Biological species | Triticum aestivum (bread wheat) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||||||||
Authors | Liao, D.-I. / Remington, S.J. | ||||||||||||
Citation | Journal: Biochemistry / Year: 1992 Title: Refined atomic model of wheat serine carboxypeptidase II at 2.2-A resolution. Authors: Liao, D.I. / Breddam, K. / Sweet, R.M. / Bullock, T. / Remington, S.J. #1: Journal: J.Biol.Chem. / Year: 1990 Title: Structure of Wheat Serine Carboxypeptidase II at 3.5 Angstroms Resolution Authors: Liao, D.-I. / Remington, S.J. #2: Journal: J.Mol.Biol. / Year: 1990 Title: Crystallization of Serine Carboxypeptidases Authors: Wilson, K.P. / Liao, D.-I. / Bullock, T. / Remington, S.J. / Breddam, K. #3: Journal: Carlsberg Res.Commun. / Year: 1987 Title: Primary Structure and Enzymatic Properties of Carboxypeptidase II from Wheat Bran Authors: Breddam, K. / Sorensen, S.B. / Svendsen, I. | ||||||||||||
History |
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Remark 700 | SHEET THE SECONDARY STRUCTURE ASSIGNMENT IS ACCORDING TO KABSCH AND SANDER (BIOPOLYMERS 22, 2577- ...SHEET THE SECONDARY STRUCTURE ASSIGNMENT IS ACCORDING TO KABSCH AND SANDER (BIOPOLYMERS 22, 2577-2637, 1983) DSSP PROGRAM EXCEPT FOR RESIDUES -1 TO 1 AND 102 TO 105. BOTH STRANDS ARE INVOLVED IN THE HYDROGEN BONDING OF A BETA SHEET, BUT NEITHER OF THEM IS ASSIGNED AS A BETA STRAND BY DSSP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sc2.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sc2.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 3sc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sc2_validation.pdf.gz | 606.4 KB | Display | wwPDB validaton report |
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Full document | 3sc2_full_validation.pdf.gz | 628.5 KB | Display | |
Data in XML | 3sc2_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 3sc2_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/3sc2 ftp://data.pdbj.org/pub/pdb/validation_reports/sc/3sc2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THERE IS NO APPARENT ELECTRON DENSITY FOR THE SIDE CHAINS OF RESIDUES GLU A 24, LYS A 163, ARG B 282, THR B 293, AND GLN B 375A. THE SIDE CHAINS ARE MODELLED WITH ZERO OCCUPANCY. 2: RESIDUES PRO A 43, PRO A 54, AND PRO A 96 ARE CIS PROLINES. |
-Components
#1: Protein | Mass: 28705.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Triticum aestivum (bread wheat) / References: UniProt: P08819, EC: 3.4.16.1 | ||||
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#2: Protein | Mass: 17192.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P08819, EC: 3.4.16.1 | ||||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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 #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.52 Å3/Da / Density % sol: 77.74 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 38081 / % possible obs: 72.9 % / Num. measured all: 103780 |
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-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.169 / Highest resolution: 2.2 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. reflection obs: 35941 / Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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