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Open data
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Basic information
Entry | Database: PDB / ID: 1naq | ||||||
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Title | Crystal structure of CUTA1 from E.coli at 1.7 A resolution | ||||||
![]() | Periplasmic divalent cation tolerance protein cutA | ||||||
![]() | ELECTRON TRANSPORT / CUTA / copper resistance / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | ![]() response to copper ion / copper ion binding / protein-containing complex / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Calderone, V. / Mangani, S. / Benvenuti, M. / Viezzoli, M.S. / Banci, L. / Bertini, I. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() Title: The evolutionarily conserved trimeric structure of CutA1 proteins suggests a role in signal transduction. Authors: Arnesano, F. / Banci, L. / Benvenuti, M. / Bertini, I. / Calderone, V. / Mangani, S. / Viezzoli, M.S. #1: ![]() Title: STRUCTURE OF PROTEIN TM1056, CUTA Authors: SAVCHENKO, A. / ZHANG, R. / JOACHIMIAK, A. / EDWARDS, A. / AKARINA, T. | ||||||
History |
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Remark 600 | HETEROGEN P-HYDROXYMERCURIBENZOIC ACID HAS BEEN ADDED TO THE PROTEIN PRIOR TO CRYSTALLISATION. IT ...HETEROGEN P-HYDROXYMERCURIBENZOIC ACID HAS BEEN ADDED TO THE PROTEIN PRIOR TO CRYSTALLISATION. IT REACTS WITH THE -SH OF FREE CYSTEINS AND, BY THE ELIMINATION OF ONE WATER MOLECULE, FORMS A COVALENT BOND BETWEEN THE S OF THE CYS AND HG WHICH IS THEN A GOOD CANDIDATE TO PERFORM A MAD EXPERIMENT. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.5 KB | Display | ![]() |
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PDB format | ![]() | 114.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 46 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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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3 |
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Unit cell |
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Details | The biological functional unit is a trimer; the asymmetric unit is made of two trimers. |
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Components
#1: Protein | Mass: 12342.025 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HG / #3: Chemical | ChemComp-MBO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.56 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Na HEPES, 2M Ammonium sulphate, 2% PEG 400, 2 mM 4-(hydroxymercuri)benzoic acid, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 14, 2002 | ||||||||||||
Radiation | Monochromator: Double crystal focussing monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→37.5 Å / Num. all: 65739 / Num. obs: 65739 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 18.95 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.7 | ||||||||||||
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.1 / Num. unique all: 9337 / Rsym value: 0.619 / % possible all: 96.3 | ||||||||||||
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 643844 | ||||||||||||
Reflection shell | *PLUS % possible obs: 96.3 % / Num. unique obs: 9337 / Num. measured obs: 90452 / Rmerge(I) obs: 0.519 |
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Processing
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Refinement | Method to determine structure: ![]() Details: At the N-terminus of all the six molecules present in the asymetric unit there are about 6-8 residues for which it's not possible to see a clear density. Among the densities belonging to ...Details: At the N-terminus of all the six molecules present in the asymetric unit there are about 6-8 residues for which it's not possible to see a clear density. Among the densities belonging to each asymmetric unit it's possible to see some extra density which could account for the presence of some crystalline PEG fragments.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.738 Å2
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Refine analyze | Luzzati sigma a obs: 0.055714 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.79 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.203 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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