+Open data
-Basic information
Entry | Database: PDB / ID: 1s7m | ||||||
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Title | Crystal Structure of HiaBD1 | ||||||
Components | Hia | ||||||
Keywords | CELL ADHESION / adhesion / homotrimer / autotransporter | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Initial phasing: MAD of two Met sites introduced protein crystal, then Molecular replacement on native crystal / Resolution: 2.1 Å | ||||||
Authors | Yeo, H.J. / Cotter, S.E. / Laarmann, S. / Juehne, T. / St Geme, J.W. / Waksman, G. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Structural basis for host recognition by the Haemophilus influenzae Hia autotransporter. Authors: Yeo, H.J. / Cotter, S.E. / Laarmann, S. / Juehne, T. / St Geme, J.W. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s7m.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s7m.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 1s7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/1s7m ftp://data.pdbj.org/pub/pdb/validation_reports/s7/1s7m | 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 18022.633 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: strain 11 / Gene: hia / Plasmid: pGEX6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q48152 #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: 3.29 Å3/Da / Density % sol: 62.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.99187 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 30, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 72387 / Num. obs: 72387 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 25.05 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: Initial phasing: MAD of two Met sites introduced protein crystal, then Molecular replacement on native crystal Starting model: SeMetHiaBD1(HiaBD1 variant genrated for Se MAD phasing) Resolution: 2.1→44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 409136.36 / 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: 46.5725 Å2 / ksol: 0.355562 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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