+Open data
-Basic information
Entry | Database: PDB / ID: 3aeh | ||||||
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Title | Integral membrane domain of autotransporter Hbp | ||||||
Components | Hemoglobin-binding protease hbp autotransporter | ||||||
Keywords | HYDROLASE / BETA-BARREL / AUTO-PROTEOLYTIC / REACTION INTERMEDIATE / MUTANT / Cell membrane / Cell outer membrane / Membrane / Protease / Secreted / Serine protease / Transmembrane / Virulence / INTEIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Tajima, N. / Park, S.-Y. / Tame, J.R.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: A novel intein-like autoproteolytic mechanism in autotransporter proteins. Authors: Tajima, N. / Kawai, F. / Park, S.Y. / Tame, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aeh.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aeh.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 3aeh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/3aeh ftp://data.pdbj.org/pub/pdb/validation_reports/ae/3aeh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | 1 |
-Components
#1: Protein | Mass: 34015.469 Da / Num. of mol.: 2 / Fragment: barrel domain / Mutation: N1100D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hbp / Production host: Escherichia coli (E. coli) References: UniProt: O88093, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES pH 7.0, 55% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2009 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.9 Å / Num. obs: 46742 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.051 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.149 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.725 Å2
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Refinement step | Cycle: LAST / Resolution: 2→48.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2154 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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