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Yorodumi- PDB-1x6r: Structure 5: room temperature crystal structure of the truncated ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x6r | ||||||
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Title | Structure 5: room temperature crystal structure of the truncated pak pilin from Pseudomonas aeruginosa at 1.80A resolution | ||||||
Components | Fimbrial protein | ||||||
Keywords | STRUCTURAL PROTEIN / TYPE IV PILIN / LECTIN / ADHESIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Dunlop, K.V. / Irvin, R.T. / Hazes, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Pros and cons of cryocrystallography: should we also collect a room-temperature data set? Authors: Dunlop, K.V. / Irvin, R.T. / Hazes, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x6r.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x6r.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 1x6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/1x6r ftp://data.pdbj.org/pub/pdb/validation_reports/x6/1x6r | HTTPS FTP |
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-Related structure data
Related structure data | 1x6pC 1x6qC 1x6xC 1x6yC 1x6zC 1dzoS 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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Details | Protein assembles to form a fiber. See PDB codes 1DZO and 1AY2 |
-Components
#1: Protein | Mass: 12696.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K / Cellular location: EXTRACELLULAR FILAMENTOUS APPENDAGE / Gene: pilA, fimA / Plasmid: PRLD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02973 |
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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: 2.1 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.2 Details: 60% Ammonium Sulfate, 0.1M Hepes, pH 8.2, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 10, 2001 / Details: SUPPER MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→23.6 Å / Num. all: 10367 / Num. obs: 10367 / % possible obs: 76 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 11.59 |
Reflection shell | Resolution: 1.8→1.85 Å / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DZO Resolution: 1.82→23.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.192 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.103 / ESU R Free: 0.103 / 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: 14.746 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→23.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.87 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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