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Yorodumi- PDB-1kdb: STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kdb | ||||||
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Title | STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING | ||||||
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: 1.9 Å | ||||||
Authors | Hodel, A. / Fox, R.O. | ||||||
Citation | Journal: Protein Sci. / Year: 1995 Title: Stabilization of a strained protein loop conformation through protein engineering. Authors: Hodel, A. / Kautz, R.A. / Fox, R.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kdb.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kdb.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 1kdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kdb_validation.pdf.gz | 360.8 KB | Display | wwPDB validaton report |
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Full document | 1kdb_full_validation.pdf.gz | 363.3 KB | Display | |
Data in XML | 1kdb_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1kdb_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/1kdb ftp://data.pdbj.org/pub/pdb/validation_reports/kd/1kdb | 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: 16843.264 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.8 % | ||||||||||||||||||||
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Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
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: 1.9 Å / Lowest resolution: 6 Å / Num. obs: 10190 / % possible obs: 99 % / Rmerge(I) obs: 0.05 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.188 / Rfactor obs: 0.188 / Highest resolution: 1.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.62 |