+Open data
-Basic information
Entry | Database: PDB / ID: 1ak0 | |||||||||
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Title | P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG | |||||||||
Components | P1 NUCLEASE | |||||||||
Keywords | ENDONUCLEASE / P1 NUCLEASE / REACTION MECHANISM / THIOPHOSPHORYLATED OLIGONUCLEOTIDES / GLYCOSYLATED PROTEIN | |||||||||
Function / homology | Function and homology information Aspergillus nuclease S1 / DNA catabolic process / endonuclease activity / nucleic acid binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Penicillium citrinum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Romier, C. / Suck, D. | |||||||||
Citation | Journal: Proteins / Year: 1998 Title: Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs. Authors: Romier, C. / Dominguez, R. / Lahm, A. / Dahl, O. / Suck, D. #1: Journal: Embo J. / Year: 1991 Title: Crystal Structure of Penicillium Citrinum P1 Nuclease at 2.8 A Resolution Authors: Volbeda, A. / Lahm, A. / Sakiyama, F. / Suck, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ak0.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ak0.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ak0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ak0_validation.pdf.gz | 654.3 KB | Display | wwPDB validaton report |
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Full document | 1ak0_full_validation.pdf.gz | 664.4 KB | Display | |
Data in XML | 1ak0_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1ak0_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1ak0 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1ak0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29251.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium citrinum (fungus) / References: UniProt: P24289, Aspergillus nuclease S1 |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar |
-Non-polymers , 4 types, 162 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-ADS / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.65 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.3 / Details: PEG 6000 12 - 20% 25 MM NA ACETATE PH 5.3 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 27854 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.068 |
Reflection shell | Resolution: 1.8→1.95 Å / Rsym value: 0.247 / % possible all: 89.9 |
Reflection | *PLUS Num. measured all: 119199 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 89.9 % / Rmerge(I) obs: 0.247 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Displacement parameters | Biso mean: 22.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.8 Å2 |