+Open data
-Basic information
Entry | Database: PDB / ID: 3fq1 | ||||||
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Title | Azurin C112D/M121I | ||||||
Components | Azurin | ||||||
Keywords | ELECTRON TRANSPORT / Copper Binding / Copper / Metal-binding / Periplasm / Transport | ||||||
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: 1.9 Å | ||||||
Authors | Lancaster, K.M. / Gray, H.B. | ||||||
Citation | Journal: Nat Chem / Year: 2009 Title: Type Zero Copper Proteins. Authors: Lancaster, K.M. / Debeer George, S. / Yokoyama, K. / Richards, J.H. / Gray, H.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fq1.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fq1.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fq1_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 3fq1_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 3fq1_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 3fq1_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/3fq1 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/3fq1 | HTTPS FTP |
-Related structure data
Related structure data | 3fpyC 3fq2C 3fqyC 1ag0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 13955.705 Da / Num. of mol.: 1 / Mutation: C112D, M121I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00282 | ||||
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#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25% PEG 4000, 0.1M sodium acetate pH 5.6, 0.1 M tris pH 8, 0.1 M lithium nitrate, 0.01 M copper(II) sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2008 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.992 Å / Num. all: 13824 / Num. obs: 13824 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.0203 / % possible all: 75.42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AG0 Resolution: 1.9→19.99 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.803 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.165 / 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: 26.688 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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