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Yorodumi- PDB-1enc: CRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1enc | ||||||
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Title | CRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE TERNARY COMPLEX OF THE ASP 21->GLU MUTANT OF STAPHYLOCOCCAL NUCLEASE. IMPLICATIONS FOR CATALYSIS AND LIGAND BINDING | ||||||
Components | STAPHYLOCOCCAL NUCLEASEMicrococcal nuclease | ||||||
Keywords | HYDROLASE(PHOSPHORIC DIESTER) | ||||||
Function / homology | Function and homology information endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.95 Å | ||||||
Authors | Libson, A. / Gittis, A. / Lattman, E.E. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Crystal structures of the binary Ca2+ and pdTp complexes and the ternary complex of the Asp21-->Glu mutant of staphylococcal nuclease. Implications for catalysis and ligand binding. Authors: Libson, A.M. / Gittis, A.G. / Lattman, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1enc.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1enc.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 1enc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/1enc ftp://data.pdbj.org/pub/pdb/validation_reports/en/1enc | 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: CIS PROLINE - PRO 117 |
-Components
#1: Protein | Mass: 16857.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / References: UniProt: P00644, micrococcal nuclease |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-THP / |
#4: Water | ChemComp-HOH / |
Compound details | ASP 21 IS LIGAND OF ACTIVE SITE CA2+ IN THE WILD TYPE STRUCTURE. THE D21E MUTANT STILL BINDS CA2+, ...ASP 21 IS LIGAND OF ACTIVE SITE CA2+ IN THE WILD TYPE STRUCTURE. THE D21E MUTANT STILL BINDS CA2+, BUT MOVES THE METAL ION 1.5 ANGSTROMS OUT OF THE ACTIVE SITE POCKET. THIS MOVEMENT CAUSES GLU 43 TO BECOME AN INNER SPHERE LIGAND OF CA2+ AND PERTURBS THE NORMAL WATER COORDINATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.96 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 9999 Å / Num. obs: 9811 / % possible obs: 85 % / Num. measured all: 44141 / Rmerge(I) obs: 0.046 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.174 / Rfactor obs: 0.174 / Highest resolution: 1.95 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.95 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 6 Å / Num. reflection obs: 9312 / Rfactor obs: 0.174 / Rfactor Rwork: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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