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Yorodumi- PDB-2xv3: Pseudomonas aeruginosa Azurin with mutated metal-binding loop seq... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xv3 | ||||||
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Title | Pseudomonas aeruginosa Azurin with mutated metal-binding loop sequence (CAAAAHAAAAM), chemically reduced, pH5.3 | ||||||
Components | AZURIN | ||||||
Keywords | ELECTRON TRANSPORT / CUPREDOXIN FOLD | ||||||
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: 2.3 Å | ||||||
Authors | Li, C. / Sato, K. / Monari, S. / Salard, I. / Sola, M. / Banfield, M.J. / Dennison, C. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2011 Title: Metal-Binding Loop Length is a Determinant of the Pka of a Histidine Ligand at a Type 1 Copper Site Authors: Li, C. / Sato, K. / Monari, S. / Salard, I. / Sola, M. / 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 | 2xv3.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xv3.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/2xv3 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/2xv3 | HTTPS FTP |
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-Related structure data
Related structure data | 2xv0C 2xv2C 3fszS 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 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / 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 MUTANT 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: 2.04 Å3/Da / Density % sol: 39.78 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 10MM TRI-SODIUM CITRATE, 33% PEG6000, 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: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.49 Å / Num. obs: 9493 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FSZ Resolution: 2.3→29.48 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.862 / SU B: 9.009 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.687 / ESU R Free: 0.301 / 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: 19.201 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.48 Å
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Refine LS restraints |
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