[English] 日本語
Yorodumi- PDB-1bcr: COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bcr | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, ANTIPAIN, AND ARGININE AT ROOM TEMPERATURE | |||||||||||||||
Components |
| |||||||||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / MICROBIAL PEPTIDE ALDEHYDE INHIBITOR / SERINE PROTEASE-INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||||||||
Function / homology | Function and homology information carboxypeptidase D / serine-type carboxypeptidase activity / proteolysis Similarity search - Function | |||||||||||||||
Biological species | Triticum aestivum (bread wheat) Actinobacteria (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | |||||||||||||||
Authors | Bullock, T.L. / Remington, S.J. | |||||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Peptide aldehyde complexes with wheat serine carboxypeptidase II: implications for the catalytic mechanism and substrate specificity. Authors: Bullock, T.L. / Breddam, K. / Remington, S.J. #1: Journal: Biochemistry / Year: 1994 Title: Structure of the Complex of L-Benzylsuccinate with Wheat Serine Carboxypeptidase at 2.0 Angstrom Resolution Authors: Bullock, T.L. / Branchaud, B. / Remington, S.J. #2: Journal: Biochemistry / Year: 1992 Title: Refined Atomic Model of Wheat Serine Carboxypeptidase II at 2.2 Angstrom Resolution Authors: Liao, D.I. / Breddam, K. / Sweet, R.M. / Bullock, T. / Remington, S.J. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bcr.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bcr.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bcr_validation.pdf.gz | 560.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1bcr_full_validation.pdf.gz | 582.5 KB | Display | |
Data in XML | 1bcr_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1bcr_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/1bcr ftp://data.pdbj.org/pub/pdb/validation_reports/bc/1bcr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO A 43 / 2: CIS PROLINE - PRO A 54 / 3: CIS PROLINE - PRO A 96 |
-Components
-SERINE CARBOXYPEPTIDASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 29180.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / Tissue: WHEAT GERM / References: UniProt: P08819, carboxypeptidase D |
---|---|
#2: Protein | Mass: 17995.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / Tissue: WHEAT GERM / References: UniProt: P08819, carboxypeptidase D |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | |
---|
-Sugars , 3 types, 3 molecules
#4: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[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: 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 |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 193 molecules
#7: Chemical | ChemComp-ARG / |
---|---|
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 5.31 Å3/Da / Density % sol: 76.82 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
Diffraction source | Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Redundancy: 2.23 % / Rmerge(I) obs: 0.054 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 29444 / % possible obs: 86 % / Num. measured all: 65638 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 71 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→21 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→21 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|