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Yorodumi- PDB-4iuw: Crystal structure of PEPO from Lactobacillus rhamnosis HN001 (DR20) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iuw | ||||||
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Title | Crystal structure of PEPO from Lactobacillus rhamnosis HN001 (DR20) | ||||||
Components | Neutral endopeptidase | ||||||
Keywords | HYDROLASE / Neutral peptidase / ZN Metallopeptidase / Endopeptidase | ||||||
Function / homology | Function and homology information Neutral endopeptidase; domain 2 / Neutral endopeptidase , domain2 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Lactobacillus rhamnosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Anderson, B.F. / Knapp, K.M. / Holland, R. / Norris, G.E. / Christensson, C. / Bratt, H. / Collins, L.J. / Coolbear, T. / Lubbers, M.W. / Toole, P.W.O. ...Anderson, B.F. / Knapp, K.M. / Holland, R. / Norris, G.E. / Christensson, C. / Bratt, H. / Collins, L.J. / Coolbear, T. / Lubbers, M.W. / Toole, P.W.O. / Reid, J.R. / Jameson, G.B. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of PEPO from Lactobacillus rhamnosis HN001 (DR20) Authors: Anderson, B.F. / Knapp, K.M. / Holland, R. / Norris, G.E. / Christensson, C. / Bratt, H. / Collins, L.J. / Coolbear, T. / Lubbers, M.W. / O Toole, P.W. / Reid, J.R. / Jameson, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iuw.cif.gz | 155.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iuw.ent.gz | 120.1 KB | Display | PDB format |
PDBx/mmJSON format | 4iuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iuw_validation.pdf.gz | 482.5 KB | Display | wwPDB validaton report |
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Full document | 4iuw_full_validation.pdf.gz | 486.9 KB | Display | |
Data in XML | 4iuw_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 4iuw_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/4iuw ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4iuw | 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 71024.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: HN001 (Dr20) / Gene: LRH_04328 / Plasmid: LB004 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): cremoris NZ 9000 References: UniProt: B5QNF0, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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-Non-polymers , 7 types, 640 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-CIT / | ||||||
#4: Chemical | ChemComp-NA / | ||||||
#5: Chemical | #6: Chemical | ChemComp-CO3 / #7: Chemical | ChemComp-OXD / | #8: 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: 2.01 Å3/Da / Density % sol: 38.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.0M LITHIUM SULPHATE MONOHYDRATE, 0.1M TRI-SODIUM CITRATE DEHYDRATE, 0.1M AMMONIUM SULPHATE, pH 5.6, 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: Mar 11, 2005 / 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: 1.85→39.24 Å / Num. all: 46976 / Num. obs: 46976 / % possible obs: 79.6 % / Redundancy: 6.13 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZUK Resolution: 1.85→39.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.861 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.165 / 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: 21.977 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→39.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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