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Yorodumi- PDB-2arz: Crystal Structure of Protein of Unknown Function from Pseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2arz | ||||||
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Title | Crystal Structure of Protein of Unknown Function from Pseudomonas aeruginosa | ||||||
Components | hypothetical protein PA4388Hypothesis | ||||||
Keywords | UNKNOWN FUNCTION / hypothetical protein / structural genomics / MCSG / Pseudomonas aeruginosa / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information PNP-oxidase-like / Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Split barrel-like / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll ...PNP-oxidase-like / Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / Split barrel-like / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Alpha-Beta Barrel / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Nocek, B. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of hypothetical protein from Pseudomonas aeruginosa Authors: Nocek, B. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2arz.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2arz.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 2arz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/2arz ftp://data.pdbj.org/pub/pdb/validation_reports/ar/2arz | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | X-ray crystallography data suggests dimer |
-Components
#1: Protein | Mass: 27306.908 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HW16 #2: Chemical | #3: Chemical | #4: 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: 2.6 Å3/Da / Density % sol: 52.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.1MBis-Tris PH6.4, 0.2M CaCl2, 16.5% PEG5K, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 38922 / Num. obs: 38922 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 22.03 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→33.56 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.218 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. OTHER SOFTWARE USED IN THE SOLUTION OF THIS STRUCTRE INCLUDES SHELXD, SHELXE, MLPHARE, DM, SOLVE/RESOLVE, O, COOT, AND CCP4
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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: 36.665 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 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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