+Open data
-Basic information
Entry | Database: PDB / ID: 3urd | ||||||
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Title | T181A mutant of alpha-Lytic Protease | ||||||
Components | Alpha-lytic proteaseAlpha-lytic endopeptidase | ||||||
Keywords | HYDROLASE / Serine protease | ||||||
Function / homology | Function and homology information alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Lysobacter enzymogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å | ||||||
Authors | Kelch, B.A. / Agard, D.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Functional modulation of a protein folding landscape via side-chain distortion. Authors: Kelch, B.A. / Salimi, N.L. / Agard, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3urd.cif.gz | 103.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3urd.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 3urd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/3urd ftp://data.pdbj.org/pub/pdb/validation_reports/ur/3urd | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19845.105 Da / Num. of mol.: 1 / Fragment: UNP residues 200-397 / Mutation: T132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Gene: alpha-LP / Production host: Escherichia coli (E. coli) / References: UniProt: P00778, alpha-lytic endopeptidase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #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: 2.5 Å3/Da / Density % sol: 50.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.3 M lithium sulfate and 20 mM Tris sulfate, pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.8 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2007 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→50 Å / Num. all: 85730 / Num. obs: 85721 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10 % / Rsym value: 0.077 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.08→1.1 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.404 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.618 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.882 Å2
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Refinement step | Cycle: LAST / Resolution: 1.08→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.08→1.108 Å / Total num. of bins used: 20
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