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Yorodumi- PDB-1ena: CRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ena | ||||||
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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 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: 2.15 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 | 1ena.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ena.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ena.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ena_validation.pdf.gz | 364.8 KB | Display | wwPDB validaton report |
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Full document | 1ena_full_validation.pdf.gz | 371.3 KB | Display | |
Data in XML | 1ena_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1ena_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/1ena ftp://data.pdbj.org/pub/pdb/validation_reports/en/1ena | HTTPS FTP |
-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: 15421.900 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: 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. IN THE BINARY METAL COMPLEX, CA2+ IS 0.5 ANGSTROMS LOWER IN THE POCKET (TOWARD THR 41). GLU 43 IS AN INNER SPHERE LIGAND OF CA2+. ARG 35 IS FOUND IN A DIFFERENT ORIENTATIO |
Sequence details | SEQUENCE ADVISORY NOTICE SWISS-PROT PDB SEQRES COMMENT CONFLICT ASP 103 GLU 21 MUTATION SITE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.46 % | ||||||||||||||||||||||||||||||
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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: 2.08 Å / Lowest resolution: 6 Å / Num. obs: 7583 / % possible obs: 89 % / Num. measured all: 16727 / Rmerge(I) obs: 0.107 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.225 / Rfactor obs: 0.225 / Highest resolution: 2.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.15 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 6 Å / Num. reflection obs: 7003 / Rfactor obs: 0.225 / Rfactor Rwork: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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