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Yorodumi- PDB-3opn: The crystal structure of a putative hemolysin from Lactococcus lactis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3opn | ||||||
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Title | The crystal structure of a putative hemolysin from Lactococcus lactis | ||||||
Components | putative hemolysin | ||||||
Keywords | structural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / SGX / PSI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Zhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a putative hemolysin from Lactococcus lactis Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3opn.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3opn.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 3opn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/3opn ftp://data.pdbj.org/pub/pdb/validation_reports/op/3opn | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25981.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Strain: lactis (Ll) / Gene: L814, L81441, LL0858, yiiB / Plasmid: BC - pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) - Codon+RIL / References: UniProt: Q9CH80 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 1.81 Å3/Da / Density % sol: 31.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Ammonium sulfate, 0.1 M cacodylate trihydrate pH 6.5, 30% w/v PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→70.64 Å / Num. all: 12358 / Num. obs: 12358 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 12.96 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 33 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 19.5 / Num. unique all: 1759 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→43.162 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / σ(F): 2.55 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.676 Å2 / ksol: 0.369 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.74 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→43.162 Å
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Refine LS restraints |
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LS refinement shell |
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