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- PDB-2enb: CRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2enb | ||||||
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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 | ||||||
![]() | STAPHYLOCOCCAL NUCLEASE | ||||||
![]() | HYDROLASE(PHOSPHORIC DIESTER) | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Libson, A. / Gittis, A. / Lattman, E.E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.1 KB | Display | ![]() |
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PDB format | ![]() | 28.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.8 KB | Display | ![]() |
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Full document | ![]() | 450.2 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 7.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 117 |
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Components
#1: Protein | Mass: 15421.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-THP / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: NUC_ ...SEQUENCE ADVISORY NOTICE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 6 Å / Num. obs: 8297 / % possible obs: 80 % / Num. measured all: 37566 / Rmerge(I) obs: 0.043 |
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Processing
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Refinement | Rfactor Rwork: 0.177 / Rfactor obs: 0.177 / Highest resolution: 2.05 Å Details: IN THE BINARY COMPLEX OF THE ASP 21 GLU MUTANT OF OF STAPHYLOCOCCAL NUCLEASE, A WATER MOLECULE REPLACES CA2+ AT THE ACTIVE SITE. THERE IS 0.5 ANGSTROMS MOVEMENT OF THE INHIBITOR, PDTP, AWAY ...Details: IN THE BINARY COMPLEX OF THE ASP 21 GLU MUTANT OF OF STAPHYLOCOCCAL NUCLEASE, A WATER MOLECULE REPLACES CA2+ AT THE ACTIVE SITE. THERE IS 0.5 ANGSTROMS MOVEMENT OF THE INHIBITOR, PDTP, AWAY FROM THE ACTIVE SITE. THE SIDE CHAIN OF GLU 43 POINTS INTO BULK SOLVENT. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.05 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 6 Å / Num. reflection obs: 7556 / Rfactor obs: 0.177 / Rfactor Rwork: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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