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Yorodumi- PDB-2ft6: Structure of Cu(II)azurin with the metal-binding loop sequence "C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ft6 | ||||||
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Title | Structure of Cu(II)azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CTPHPM" | ||||||
Components | Azurin | ||||||
Keywords | ELECTRON TRANSPORT / Blue copper-binding protein / greek-key beta-barrel | ||||||
Function / homology | Function and homology information transition metal ion binding / electron transfer activity / periplasmic space / copper ion binding / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Banfield, M.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Basic requirements for a metal-binding site in a protein: The influence of loop shortening on the cupredoxin azurin. Authors: Li, C. / Yanagisawa, S. / Martins, B.M. / Messerschmidt, A. / Banfield, M.J. / Dennison, C. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Crystal structure analysis of oxidized Pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. A pH-induced conformational transition involves a peptide bond flip Authors: Nar, H. / Messerschmidt, A. / Huber, R. / van de Kamp, M. / Canters, G.W. #2: Journal: J.Am.Chem.Soc. / Year: 2004 Title: Loop-contraction mutagenesis of type 1 copper sites Authors: Yanagisawa, S. / Dennison, C. #3: Journal: J.Mol.Biol. / Year: 1994 Title: Crystal structure analysis and refinement at 2.15 A resolution of amicyanin, a type I blue copper PROTEIN, FROM THIOBACILLUS VERSUTUS Authors: Romero, A. / Nar, H. / Huber, R. / Messerschmidt, A. / Kalverda, A.P. / Canters, G.W. / Durley, R. / Mathews, F.S. | ||||||
History |
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Remark 999 | Amino acid sequence CTFPGHSALM, involving residues 132 to 141 in the amino acid database was ...Amino acid sequence CTFPGHSALM, involving residues 132 to 141 in the amino acid database was replaced with the sequence CTPHPM in the deposition |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ft6.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ft6.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ft6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/2ft6 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/2ft6 | HTTPS FTP |
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-Related structure data
Related structure data | 2ft7C 2ft8C 2ftaC 4azuS 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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Unit cell |
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Details | The biological assembly is monomeric (as found in the asymmetric unit) |
-Components
#1: Protein | Mass: 13583.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / Plasmid: Trk99a / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P00282 |
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#2: Chemical | ChemComp-CU / |
#3: 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: 1.86 Å3/Da / Density % sol: 34.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1MM MES, 20% PEG6000, 0.2M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.075 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 16, 2005 |
Radiation | Monochromator: double Si(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→32.953 Å / Num. all: 29176 / Num. obs: 29176 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 11.35 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.25→1.32 Å / % possible obs: 99.7 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 6.1 / Num. measured all: 38274 / Num. unique all: 4155 / Num. unique obs: 4155 / Rsym value: 0.291 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AZU, Chain A Resolution: 1.25→32.95 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.157 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT BUT NOT ADDED TO OUTPUT FILE
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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: 10.608 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→32.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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