+Open data
-Basic information
Entry | Database: PDB / ID: 1ouo | ||||||
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Title | Crystal structure of the periplasmic endonuclease Vvn | ||||||
Components | Nuclease | ||||||
Keywords | HYDROLASE / Non-specific endonuclease / beta-beta-alpha-metal motif | ||||||
Function / homology | Endonuclease I / Endonuclease I / deoxyribonuclease I / deoxyribonuclease I activity / His-Me finger superfamily / endonuclease activity / Endonuclease I / Endonuclease I Function and homology information | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Yuan, H.S. / Li, C.L. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site. Authors: Li, C.-L. / Hor, L.-I. / Chang, Z.-F. / Tsai, L.-C. / Yang, W.-Z. / Yuan, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ouo.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ouo.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1ouo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/1ouo ftp://data.pdbj.org/pub/pdb/validation_reports/ou/1ouo | 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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-Components
#1: Protein | Mass: 24695.891 Da / Num. of mol.: 1 / Fragment: residue 19-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q8DCA6, UniProt: Q7MHK3*PLUS, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 30.61 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, ammonium acetate, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9795, 0.9796, 0.9600 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2001 | ||||||||||||
Radiation | Monochromator: SI 111 + GE 220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→40 Å / Num. all: 9512 / Num. obs: 9127 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.822 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.075 / Net I/σ(I): 24.38 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 9.57 / Rsym value: 0.146 / % possible all: 96 | ||||||||||||
Reflection | *PLUS % possible obs: 96 % / Num. measured all: 62270 / Rmerge(I) obs: 0.075 | ||||||||||||
Reflection shell | *PLUS Highest resolution: 2.3 Å / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 9.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→26.55 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 283277.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.3607 Å2 / ksol: 0.348624 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→26.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 40 Å / Num. reflection obs: 8072 / Num. reflection Rfree: 731 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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