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Yorodumi- PDB-1uoy: The bubble protein from Penicillium brevicompactum Dierckx exudate. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uoy | ||||||
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Title | The bubble protein from Penicillium brevicompactum Dierckx exudate. | ||||||
Components | BUBBLE PROTEIN | ||||||
Keywords | EXUDATE PROTEIN / SULFUR PHASING / POTENTIAL KILLER TOXIN | ||||||
Function / homology | Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #50 / Bubble protein / Bubble superfamily / Bubble protein / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Roll / extracellular region / Mainly Beta / Bubble protein Function and homology information | ||||||
Biological species | PENICILLIUM BREVICOMPACTUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.5 Å | ||||||
Authors | Olsen, J.G. / Flensburg, C. / Olsen, O. / Seibold, M. / Bricogne, G. / Henriksen, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Solving the Structure of the Bubble Protein Using the Anomalous Sulfur Signal from Single-Crystal in-House Cu Kalpha Diffraction Data Only Authors: Olsen, J.G. / Flensburg, C. / Olsen, O. / Bricogne, G. / Henriksen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uoy.cif.gz | 22.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uoy.ent.gz | 16.4 KB | Display | PDB format |
PDBx/mmJSON format | 1uoy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/1uoy ftp://data.pdbj.org/pub/pdb/validation_reports/uo/1uoy | 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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Unit cell |
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-Components
#1: Protein | Mass: 6579.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PENICILLIUM BREVICOMPACTUM (fungus) / Variant: DIERCKX / References: UniProt: P83799*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | SEQUENCE YET TO BE DEPOSITED IN PUBLIC DATABASE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % Description: PHASING USING THE ANOMALOUS SIGNAL FROM 8 CYSTEINE SULFURS (4 DISULFIDE BRIDGES). THE IMAGE PLATE MODEL USED WAS RAXIS IV++ | |||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 5 Details: 16 MG/ML PROTEIN IN 30 MM NA-ACETATE BUFFER, PH 5.0 AT 4 DEG. | |||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 15, 2002 / Details: MAX-FLUX OPTICAL SYSTEM |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→15.2 Å / Num. obs: 11250 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 15 Å / Redundancy: 13.5 % / Num. measured all: 151997 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→15.21 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 834780.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.1916 Å2 / ksol: 0.340968 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→15.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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