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Yorodumi- PDB-4k7c: Crystal structure of pepw from lactobacillus rhamnosis hn001 (dr2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k7c | ||||||
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Title | Crystal structure of pepw from lactobacillus rhamnosis hn001 (dr20) determined as the selenomet derivative | ||||||
Components | Aminopeptidase C | ||||||
Keywords | HYDROLASE / aminopeptidase cysteine peptidase | ||||||
Function / homology | Cysteine proteinases / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / : Function and homology information | ||||||
Biological species | Lactobacillus rhamnosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Webby, C. / Knapp, K.M. / Anderson, B.F. / Norris, G.E. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of pepw from lactobacillus rhamnosis hn001 (dr20) determined as the selenomet derivative Authors: Webby, C. / Knapp, K.M. / Anderson, B.F. / Norris, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k7c.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k7c.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 4k7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k7c_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 4k7c_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 4k7c_validation.xml.gz | 24 KB | Display | |
Data in CIF | 4k7c_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/4k7c ftp://data.pdbj.org/pub/pdb/validation_reports/k7/4k7c | HTTPS FTP |
-Related structure data
Related structure data | 3zukS 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
#1: Protein | Mass: 51149.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Modified pET32 in which the Trx-His-Thrombin-Stag-Enterokinase sequence has been replaced by His-tag-rTEV Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: HN001 taxon-486408 / Gene: LRH 13711, LRH_13711 / Plasmid: pET32a / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): Cremoris NZ9000 References: UniProt: B5QNU9, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases | ||
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#2: Chemical | ChemComp-GOL / #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: 2.82 Å3/Da / Density % sol: 56.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 0.1M NaAc, 11% Peg 4K, 30% glycerol protectant, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2006 / Details: Capilliary |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→33.76 Å / Num. all: 84251 / Num. obs: 84251 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.22 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.49→1.54 Å / Redundancy: 1.12 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.2 / % possible all: 23.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3zuk Resolution: 1.66→33.76 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.199 / SU ML: 0.069 / Isotropic thermal model: Isotopic / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.437 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→33.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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