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Yorodumi- PDB-4cms: X-RAY ANALYSES OF ASPARTIC PROTEINASES IV. STRUCTURE AND REFINEME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cms | ||||||
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Title | X-RAY ANALYSES OF ASPARTIC PROTEINASES IV. STRUCTURE AND REFINEMENT AT 2.2 ANGSTROMS RESOLUTION OF BOVINE CHYMOSIN | ||||||
Components | CHYMOSIN B | ||||||
Keywords | HYDROLASE (ACID PROTEINASE) | ||||||
Function / homology | Function and homology information chymosin / digestion / aspartic-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Newman, M. / Frazao, C. / Khan, G. / Tickle, I.J. / Blundell, T.L. / Safro, M. / Andreeva, N. / Zdanov, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: X-ray analyses of aspartic proteinases. IV. Structure and refinement at 2.2 A resolution of bovine chymosin. Authors: Newman, M. / Safro, M. / Frazao, C. / Khan, G. / Zdanov, A. / Tickle, I.J. / Blundell, T.L. / Andreeva, N. #1: Journal: Biochemistry / Year: 1990 Title: Engineering Enzyme Sub-Site Specificity: Preparation, Kinetic Characterization and X-Ray Analysis at 2.0-Angstroms Resolution of Val111Phe Site-Mutated Calf Chymosin Authors: Strop, P. / Sedlacek, J. / Stys, J. / Kaderabkova, Z. / Blaha, I. / Pavlickova, L. / Pohl, J. / Fabry, M. / Kostka, V. / Newman, M. / Frazao, C. / Shearer, A. / Tickle, I.J. / Blundell, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cms.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cms.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 4cms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cms_validation.pdf.gz | 373.9 KB | Display | wwPDB validaton report |
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Full document | 4cms_full_validation.pdf.gz | 391 KB | Display | |
Data in XML | 4cms_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 4cms_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/4cms ftp://data.pdbj.org/pub/pdb/validation_reports/cm/4cms | 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: RESIDUE PRO 23 IS A CIS-PROLINE. 2: THESE RESIDUES ARE IN POORLY DEFINED REGIONS IN THE ELECTRON DENSITY MAP: GLY -2 TO VAL 1, ASN 8 TO GLN 13, ASN 158 TO SER 163, GLN 239 TO GLU 244, GLN 277 TO PHE 281, AND GLU 289 TO GLN 297. |
-Components
#1: Protein | Mass: 35672.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00794, chymosin |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.12 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 6 ℃ / pH: 6 / Method: microdialysis | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 16823 / % possible obs: 96.6 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.089 |
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-Processing
Software | Name: RESTRAIN / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→8 Å / σ(F): 2 Details: THE QUANTITY PRESENTED IN THE TEMPERATURE FACTOR FIELD IS U.
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection obs: 13089 / σ(F): 2 / Rfactor obs: 0.158 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_plane_restr / Dev ideal: 0.007 |