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Yorodumi- PDB-4e9b: Structure of Peptide Deformylase form Helicobacter Pylori in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e9b | ||||||
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Title | Structure of Peptide Deformylase form Helicobacter Pylori in complex with actinonin | ||||||
Components | Peptide deformylase 11 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBTIOR / HYDROLASE-HYDROLASE INHIBTIOR complex | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Cui, K. / Zhu, L. / Lu, W. / Huang, J. | ||||||
Citation | Journal: To be Published Title: Identification of Novel Peptide Deformylase Inhibitors from Natural Products Authors: Cui, K. / Zhu, L. / Lu, W. / Huang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e9b.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e9b.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 4e9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e9b_validation.pdf.gz | 772.9 KB | Display | wwPDB validaton report |
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Full document | 4e9b_full_validation.pdf.gz | 775.8 KB | Display | |
Data in XML | 4e9b_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 4e9b_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/4e9b ftp://data.pdbj.org/pub/pdb/validation_reports/e9/4e9b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLPQEDGVQHKEDCLEIINPKFIETGGSMMYKEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFEKEL |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21008.465 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-164 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: def, def11 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q672W7, peptide deformylase |
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-Non-polymers , 5 types, 69 molecules
#2: Chemical | ChemComp-CO / | ||
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#3: Chemical | ChemComp-BB2 / | ||
#4: Chemical | ChemComp-EPE / | ||
#5: Chemical | #6: 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: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 290 K / Method: evaporation / pH: 7.5 / Details: HEPES, MPD, pH 7.5, EVAPORATION, temperature 290K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→34.19 Å / Num. obs: 20879 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.19 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.636 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 24.725 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.19 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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