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Yorodumi- PDB-1r19: Crystal Structure Analysis of S.epidermidis adhesin SdrG binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r19 | ||||||
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Title | Crystal Structure Analysis of S.epidermidis adhesin SdrG binding to Fibrinogen (Apo structure) | ||||||
Components | fibrinogen-binding protein SdrG | ||||||
Keywords | CELL ADHESION / MSCRAMM / SdrG native | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.51 Å | ||||||
Authors | Ponnuraj, K. / Bowden, M.G. / Davis, S. / Gurusiddappa, S. / Moore, D. / Choe, D. / Xu, Y. / Hook, M. / Narayana, S.V.L. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: A "dock, lock and latch" Structural Model for a Staphylococcal Adhesin Binding to Fibrinogen Authors: Ponnuraj, K. / Bowden, M.G. / Davis, S. / Gurusiddappa, S. / Moore, D. / Choe, D. / Xu, Y. / Hook, M. / Narayana, S.V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r19.cif.gz | 203.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r19.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 1r19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r19 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r19 | HTTPS FTP |
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-Related structure data
Related structure data | 1r17SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 38522.770 Da / Num. of mol.: 4 / Fragment: SdrG ligand binding A-domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: sdrG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KI13 |
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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: 2.42 Å3/Da / Density % sol: 49.13 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 2000 MME, NaCl, MES, Pipes, Cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 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: Feb 6, 2002 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 17380 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.32 % / Rsym value: 0.084 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3.5→3.62 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.189 / % possible all: 96.4 |
Reflection | *PLUS Num. obs: 13739 / Num. measured all: 57863 / Rmerge(I) obs: 0.084 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R17 Resolution: 3.51→19.99 Å / Rfactor Rfree error: 0.012 / 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: 10 Å2 / ksol: 0.153836 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.51→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.51→3.72 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.25 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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