+Open data
-Basic information
Entry | Database: PDB / ID: 2c9p | ||||||
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Title | Cu(I)Cu(II)-CopC at pH 4.5 | ||||||
Components | COPPER RESISTANCE PROTEIN C | ||||||
Keywords | ELECTRON TRANSPORT / COPPER TRANSPORT / COPPER PROTEINS / COPPER DISSOCIATION CONSTANTS / METAL-BINDING | ||||||
Function / homology | Function and homology information copper ion transport / response to copper ion / periplasmic space / copper ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | PSEUDOMONAS SYRINGAE PV. TOMATO (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.25 Å | ||||||
Authors | Zhang, L. / Koay, M. / Maher, M.J. / Xiao, Z. / Wedd, A.G. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2006 Title: Intermolecular Transfer of Copper Ions from the Copc Protein of Pseudomonas Syringae. Crystal Structures of Fully Loaded Cu(I)Cu(II) Forms. Authors: Zhang, L. / Koay, M. / Maher, M.J. / Xiao, Z. / Wedd, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c9p.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c9p.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 2c9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c9p_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 2c9p_full_validation.pdf.gz | 428.1 KB | Display | |
Data in XML | 2c9p_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 2c9p_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c9p ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c9p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 10547.078 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS SYRINGAE PV. TOMATO (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P12376 #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-NO3 / #4: Water | ChemComp-HOH / | Compound details | FACILITATES COPPER RESISTANCE BY SEQUESTRATION OF COPPER IN THE PERIPLASM ALONG WITH THE COPPER- ...FACILITATE | |
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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: 3.09 Å3/Da / Density % sol: 59.85 % |
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Crystal grow | pH: 4.5 Details: 4.4-5.2 AMMONIUM NITRATE, 0.1 M SODIUM ACETATE PH 4.6-4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5412 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5412 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 16159 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.432 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.245 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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