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Yorodumi- PDB-2ew6: Structure of Helicobacter Pylori peptide deformylase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ew6 | ||||||
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Title | Structure of Helicobacter Pylori peptide deformylase in complex with inhibitor | ||||||
Components | peptide deformylase | ||||||
Keywords | HYDROLASE / Cobalt Helicobacter pylori peptide deformylase / inhibitor | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cai, J. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation Authors: Cai, J. / Han, C. / Hu, T. / Zhang, J. / Wu, D. / Wang, F. / Liu, Y. / Ding, J. / Chen, K. / Yue, J. / Shen, X. / Jiang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ew6.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ew6.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ew6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ew6_validation.pdf.gz | 680.8 KB | Display | wwPDB validaton report |
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Full document | 2ew6_full_validation.pdf.gz | 684.6 KB | Display | |
Data in XML | 2ew6_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 2ew6_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/2ew6 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/2ew6 | HTTPS FTP |
-Related structure data
Related structure data | 2ew5C 2ew7C 1ix1S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21008.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q672W7, peptide deformylase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-Y13 / ( |
#4: 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: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 60-70% MPD in 0.1M pH7.8 Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 25, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSCILLATION / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→12 Å / Num. all: 10780 / Num. obs: 10780 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1037 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IX1 Resolution: 2.2→11.99 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 86946.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.4434 Å2 / ksol: 0.420753 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→11.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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