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Yorodumi- PDB-1wxr: Crystal structure of Heme Binding protein, an autotransporter hem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wxr | ||||||
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Title | Crystal structure of Heme Binding protein, an autotransporter hemoglobine protease from pathogenic Escherichia coli | ||||||
Components | haemoglobin protease | ||||||
Keywords | HYDROLASE / hemoglobine protease / autotransporter / beta helix / heme uptake / SPATE | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Otto, B.R. / Sijbrandi, R. / Luirink, J. / Oudega, B. / Heddle, J.G. / Mizutani, K. / Park, S.-Y. / Tame, J.R.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal structure of heme binding protein, an autotransporter hemoglobin protease from pathogenic escherichia coli Authors: Otto, B.R. / Sijbrandi, R. / Luirink, J. / Oudega, B. / Heddle, J.G. / Mizutani, K. / Park, S.-Y. / Tame, J.R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wxr.cif.gz | 213.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wxr.ent.gz | 168.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/1wxr ftp://data.pdbj.org/pub/pdb/validation_reports/wx/1wxr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 111963.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HBP / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha / References: UniProt: O88093 |
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#2: 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: 3.8 Å3/Da / Density % sol: 67.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 6000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.2→30 Å / Num. obs: 81242 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→29.36 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.339 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.145 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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