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Yorodumi- PDB-4z2h: Serratia marcescens Chitinase B complexed with macrolide inhibitor 29 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z2h | ||||||
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Title | Serratia marcescens Chitinase B complexed with macrolide inhibitor 29 | ||||||
Components | Chitinase B | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Chitinase / Inhibitor / Macrolide / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Maita, N. / Sugawara, A. / Sunazuka, T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Creation of Customized Bioactivity within a 14-Membered Macrolide Scaffold: Design, Synthesis, and Biological Evaluation Using a Family-18 Chitinase Authors: Sugawara, A. / Maita, N. / Gouda, H. / Yamamoto, T. / Hirose, T. / Kimura, S. / Saito, Y. / Nakano, H. / Kasai, T. / Nakano, H. / Shiomi, K. / Hirono, S. / Watanabe, T. / Taniguchi, H. / Omura, S. / Sunazuka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z2h.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z2h.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 4z2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z2h_validation.pdf.gz | 783.1 KB | Display | wwPDB validaton report |
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Full document | 4z2h_full_validation.pdf.gz | 784.8 KB | Display | |
Data in XML | 4z2h_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 4z2h_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/4z2h ftp://data.pdbj.org/pub/pdb/validation_reports/z2/4z2h | HTTPS FTP |
-Related structure data
Related structure data | 4z2gC 4z2iC 4z2jC 4z2kC 4z2lC 3wd0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 55925.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiB / Plasmid: pTrcHisB / Production host: Escherichia coli DH5alpha (bacteria) / Strain (production host): DH5alpha / References: UniProt: P11797, chitinase | ||||
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#2: Chemical | ChemComp-M6A / ( | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / | #5: 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: 4.23 Å3/Da / Density % sol: 70.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Hepes-Na pH7.0, 0.8M ammonium sulfate, 5% (v/v) glycerol PH range: 7.0-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→40 Å / Num. all: 40914 / Num. obs: 40914 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.35→2.4 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WD0 Resolution: 2.35→39.3 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.078 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.158 / 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: 22.476 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→39.3 Å
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Refine LS restraints |
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