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- PDB-7z3f: Crystal structure of the cupredoxin AcoP from Acidithiobacillus f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z3f | ||||||
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Title | Crystal structure of the cupredoxin AcoP from Acidithiobacillus ferrooxidans, oxidized form | ||||||
![]() | AcoP | ||||||
![]() | METAL BINDING PROTEIN / cupredoxin / copper-binding | ||||||
Function / homology | Cupredoxin / metal ion binding / ACETATE ION / COPPER (II) ION / EfeO-type cupredoxin-like domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leone, P. / Sciara, G. / Ilbert, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features. Authors: Roger, M. / Leone, P. / Blackburn, N.J. / Horrell, S. / Chicano, T.M. / Biaso, F. / Giudici-Orticoni, M.T. / Abriata, L.A. / Hura, G.L. / Hough, M.A. / Sciara, G. / Ilbert, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.3 KB | Display | ![]() |
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PDB format | ![]() | 93.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z3bSC ![]() 7z3gC ![]() 7z3iC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 43 - 180 / Label seq-ID: 31 - 168
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19105.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: DN052_11965 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 135 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100mM potassium acetate, 10mM potassium chloride, 50mM MES, 50mM Tris, 50mM Hepes, 34-44% PEG3000 PH range: 6.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 34624 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.987 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Num. unique obs: 4976 / CC1/2: 0.485 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7Z3B Resolution: 1.7→38.26 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.511 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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 max: 64.31 Å2 / Biso mean: 29.042 Å2 / Biso min: 15.38 Å2
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Refinement step | Cycle: final / Resolution: 1.7→38.26 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 4002 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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