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Yorodumi- PDB-1tu9: Crystal Structure of a Protein PA3967, a Structurally Highly Homo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tu9 | ||||||
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Title | Crystal Structure of a Protein PA3967, a Structurally Highly Homologous to a Human Hemoglobin, from Pseudomonas aeruginosa PAO1 | ||||||
Components | hypothetical protein PA3967 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Heme / hemoglobin / Pseudomonas aeruginosa PAO1 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å | ||||||
Authors | Kim, Y. / Joachimiak, A. / Skarina, T. / Egorova, O. / Bochkarev, A. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of PA3967 from Pseudomonas aeruginosa PAO1, a Hypothetical Protein which is highly homologous to human Hemoglobin in structure. Authors: Kim, Y. / Joachimiak, A. / Skarina, T. / Egorova, O. / Bochkarev, A. / Savchenko, A. / Edwards, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tu9.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tu9.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tu9_validation.pdf.gz | 850.5 KB | Display | wwPDB validaton report |
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Full document | 1tu9_full_validation.pdf.gz | 852.1 KB | Display | |
Data in XML | 1tu9_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1tu9_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/1tu9 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/1tu9 | HTTPS FTP |
-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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15065.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9HX49 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-PPI / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: PEG3350, sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.2→45.64 Å / Num. all: 47042 / Num. obs: 45270 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.2 | ||||||||||||||||||
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.7 / % possible all: 75.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.2→45.64 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.248 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.409 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.2→45.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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