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Yorodumi- PDB-5pep: X-RAY ANALYSES OF ASPARTIC PROTEASES. II. THREE-DIMENSIONAL STRUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5pep | |||||||||
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Title | X-RAY ANALYSES OF ASPARTIC PROTEASES. II. THREE-DIMENSIONAL STRUCTURE OF THE HEXAGONAL CRYSTAL FORM OF PORCINE PEPSIN AT 2.3 ANGSTROMS RESOLUTION | |||||||||
Components | PEPSIN | |||||||||
Keywords | HYDROLASE(ACID PROTEINASE) | |||||||||
Function / homology | Function and homology information Surfactant metabolism / pepsin A / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.34 Å | |||||||||
Authors | Cooper, J.B. / Khan, G. / Taylor, G. / Tickle, I.J. / Blundell, T.L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1990 Title: X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution. Authors: Cooper, J.B. / Khan, G. / Taylor, G. / 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 | 5pep.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5pep.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 5pep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/5pep ftp://data.pdbj.org/pub/pdb/validation_reports/pe/5pep | HTTPS FTP |
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-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: REGIONS WITH HIGH THERMAL FACTORS ARE 240 - 245, 278 - 283, AND 294 - 298. | ||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34469.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00791, pepsin A |
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#2: Water | ChemComp-HOH / |
Sequence details | THE OLD SEQUENCE FOR PORCINE PEPSIN HAD A RESIDUE AT POSITION 230 WHICH IS NOW KNOWN NOT TO EXIST. ...THE OLD SEQUENCE FOR PORCINE PEPSIN HAD A RESIDUE AT POSITION 230 WHICH IS NOW KNOWN NOT TO EXIST. THE OLD NUMBERING (228-229-231-232) HAS BEEN USED IN THIS ENTRY FOR HISTORICAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.4 % | |||||||||||||||
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Crystal grow | *PLUS pH: 3.6 / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.34 Å / Num. obs: 15613 / Observed criterion σ(I): 3 / Num. measured all: 51501 / Rmerge(I) obs: 0.096 |
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-Processing
Software | Name: RESTRAIN / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.34→10 Å / Rfactor obs: 0.196 Details: ISOTROPIC UISO VALUES ARE PROVIDED IN THE FIELD THAT USUALLY CONTAINS B VALUES. THERE IS NO APPARENT DENSITY FOR A PHOSPHATE COVALENTLY ATTACHED TO RESIDUE SER 68. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.34 Å / Lowest resolution: 10 Å / Rfactor obs: 0.196 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Num. reflection obs: 905 / Rfactor obs: 0.16 |