+Open data
-Basic information
Entry | Database: PDB / ID: 3lum | ||||||
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Title | Structure of ulilysin mutant M290L | ||||||
Components | Ulilysin | ||||||
Keywords | HYDROLASE / metallopeptidase / metal ion binding / calcium ion binding / Calcium / Disulfide bond / Metal-binding / Metalloprotease / Protease / Zinc / Zymogen | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metallopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Methanosarcina acetivorans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Tallant, C. / Garcia-Castellanos, R. / Baumann, U. / Gomis-Ruth, F.X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: On the relevance of the Met-turn methionine in metzincins. Authors: Tallant, C. / Garcia-Castellanos, R. / Baumann, U. / Gomis-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lum.cif.gz | 253.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lum.ent.gz | 200 KB | Display | PDB format |
PDBx/mmJSON format | 3lum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lum_validation.pdf.gz | 491.4 KB | Display | wwPDB validaton report |
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Full document | 3lum_full_validation.pdf.gz | 496.9 KB | Display | |
Data in XML | 3lum_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 3lum_validation.cif.gz | 82.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/3lum ftp://data.pdbj.org/pub/pdb/validation_reports/lu/3lum | HTTPS FTP |
-Related structure data
Related structure data | 3lunC 2ckiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29016.096 Da / Num. of mol.: 4 / Fragment: UNP residues 61-322 / Mutation: M290L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: MA_3214 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star References: UniProt: Q8TL28, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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-Non-polymers , 6 types, 1466 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ARG / #6: Chemical | ChemComp-VAL / #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: 2.28 Å3/Da / Density % sol: 45.94 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.7 Å / Num. obs: 115779 / Redundancy: 9 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.036 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 7.9 / Num. unique all: 115779 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CKI Resolution: 1.7→46.28 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.553 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / 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: 10.782 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→46.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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