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Yorodumi- PDB-3ft0: Pseudomonas aeruginosa Azurin with mutated metal-binding loop seq... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ft0 | ||||||
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Title | Pseudomonas aeruginosa Azurin with mutated metal-binding loop sequence (CAAAAHAAAAM), chemically reduced | ||||||
Components | Azurin | ||||||
Keywords | METAL BINDING PROTEIN / cupredoxin-fold / metal binding / protein:protein interaction | ||||||
Function / homology | Function and homology information transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Banfield, M.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Metal-binding loop length and not sequence dictates structure. Authors: Sato, K. / Li, C. / Salard, I. / Thompson, A.J. / Banfield, M.J. / Dennison, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ft0.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ft0.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ft0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ft0_validation.pdf.gz | 425.7 KB | Display | wwPDB validaton report |
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Full document | 3ft0_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 3ft0_validation.xml.gz | 14 KB | Display | |
Data in CIF | 3ft0_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/3ft0 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/3ft0 | HTTPS FTP |
-Related structure data
Related structure data | 3fs9C 3fsaC 3fsvC 3fswC 3fszSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13856.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu, PA4922 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00282 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | METAL BINDING LOOP MUTATED TO CAAAAHAAAA | |
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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: 2.08 Å3/Da / Density % sol: 40.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 10mM tri-sodium citrate, 33% PEG 6000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2007 |
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→23.1 Å / Num. all: 17866 / Num. obs: 17866 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2509 / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FSZ Resolution: 1.8→21.75 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.311 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.175 / 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: 17.726 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→21.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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