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Open data
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Basic information
Entry | Database: PDB / ID: 5fej | ||||||
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Title | CopM in the Cu(I)-bound form | ||||||
![]() | CopM | ||||||
![]() | METAL BINDING PROTEIN / copper-binding protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Zhao, S. / Wang, X. / Liu, L. | ||||||
![]() | ![]() Title: Structural basis for copper/silver binding by the Synechocystis metallochaperone CopM. Authors: Zhao, S. / Wang, X. / Niu, G. / Dong, W. / Wang, J. / Fang, Y. / Lin, Y. / Liu, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.3 KB | Display | ![]() |
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PDB format | ![]() | 97.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.2 KB | Display | ![]() |
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Full document | ![]() | 470.7 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ffaC ![]() 5ffbC ![]() 5ffcC ![]() 5ffdC ![]() 5ffeC ![]() 3bt5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20381.482 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CU1 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.72 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1M MES 6.0, 20% PEG 2000 MME, 1mM CuSO4, 10mM Vitamin C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 22448 / % possible obs: 99.6 % / Redundancy: 3.1 % / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BT5 Resolution: 2.5→36.939 Å / FOM work R set: 0.7758 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.59 Å2 / Biso mean: 16.62 Å2 / Biso min: 6.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→36.939 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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