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Yorodumi- PDB-1bpm: DIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bpm | ||||||
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Title | DIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BINDING SITES IN BOVINE LENS LEUCINE AMINOPEPTIDASE BY X-RAY CRYSTALLOGRAPHY | ||||||
Components | LEUCINE AMINOPEPTIDASELeucyl aminopeptidase | ||||||
Keywords | HYDROLASE(ALPHA-AMINOACYLPEPTIDE) | ||||||
Function / homology | Function and homology information cysteinylglycine-S-conjugate dipeptidase / prolyl aminopeptidase / leucyl aminopeptidase / dipeptidase activity / metalloaminopeptidase activity / carboxypeptidase activity / disordered domain specific binding / manganese ion binding / peptidase activity / mitochondrion ...cysteinylglycine-S-conjugate dipeptidase / prolyl aminopeptidase / leucyl aminopeptidase / dipeptidase activity / metalloaminopeptidase activity / carboxypeptidase activity / disordered domain specific binding / manganese ion binding / peptidase activity / mitochondrion / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Kim, H. / Lipscomb, W.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Differentiation and identification of the two catalytic metal binding sites in bovine lens leucine aminopeptidase by x-ray crystallography. Authors: Kim, H. / Lipscomb, W.N. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Structure Determination and Refinement of Bovine Lens Leucine Aminopeptidase and its Complex with Bestatin Authors: Burley, S.K. / David, P.R. / Sweet, R.M. / Taylor, A. / Lipscomb, W.N. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990 Title: Molecular Structure of Leucine Aminopeptidase at 2.7-Angstroms Resolution Authors: Burley, S.K. / David, P.R. / Taylor, A. / Lipscomb, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bpm.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bpm.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/1bpm ftp://data.pdbj.org/pub/pdb/validation_reports/bp/1bpm | HTTPS FTP |
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-Related structure data
-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 471 IS A CIS PROLINE. |
-Components
#1: Protein | Mass: 52942.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: LENS / References: UniProt: P00727, leucyl aminopeptidase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.92 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 30 Å / Num. obs: 13523 / % possible obs: 98 % / Rmerge(I) obs: 0.162 / Num. measured all: 134829 |
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-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||
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Refinement | Rfactor Rwork: 0.189 / Highest resolution: 2.9 Å Details: ONE OF THE ACTIVE SITE ZINC IONS HAS BEEN REPLACED BY A MAGNESIUM ION AS DETERMINED FROM X-RAY DIFFRACTION DATA COLLECTED AT -150 DEGREES C. | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.9 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 10 Å / Num. reflection obs: 10797 / σ(I): 2 / Rfactor obs: 0.189 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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