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Yorodumi- PDB-3irp: Crystal structure of functional region of UafA from Staphylococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3irp | ||||||
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Title | Crystal structure of functional region of UafA from Staphylococcus saprophyticus at 1.50 angstrom resolution | ||||||
Components | Uro-adherence factor A | ||||||
Keywords | CELL ADHESION / DEv-IgG fold / Cell wall / Hemagglutinin / Peptidoglycan-anchor / Secreted / Virulence | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus saprophyticus subsp. saprophyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Tanaka, Y. / Shouji, Y. / Matsuoka, E. / Kuroda, M. / Tanaka, I. / Yao, M. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding Authors: Matsuoka, E. / Tanaka, Y. / Kuroda, M. / Shouji, Y. / Ohta, T. / Tanaka, I. / Yao, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3irp.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3irp.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 3irp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3irp_validation.pdf.gz | 438.8 KB | Display | wwPDB validaton report |
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Full document | 3irp_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 3irp_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 3irp_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/3irp ftp://data.pdbj.org/pub/pdb/validation_reports/ir/3irp | HTTPS FTP |
-Related structure data
Related structure data | 3irzC 3is1SC 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: 47658.391 Da / Num. of mol.: 1 / Fragment: functional region, residues 393-811 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus saprophyticus subsp. saprophyticus (bacteria) Strain: ATCC 15305 / Gene: uafA, SSP0135 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q4A0V8 | ||||
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#2: Chemical | #3: Chemical | ChemComp-K / #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: 2.3 Å3/Da / Density % sol: 46.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 30% PEG MME2000, 70mM potassium thiocyanate, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 68192 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.048 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.7 % / Num. unique all: 6814 / Rsym value: 0.149 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IS1 Resolution: 1.5→19.18 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.976 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.073 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.662 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.503→1.542 Å / Total num. of bins used: 20
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