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- PDB-4a68: Mutations in the neighbourhood of CotA-laccase trinuclear site: D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a68 | ||||||
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Title | Mutations in the neighbourhood of CotA-laccase trinuclear site: D116N mutant | ||||||
![]() | SPORE COAT PROTEIN A | ||||||
![]() | OXIDOREDUCTASE / MULTI-COPPER OXIDASE / OXIDOREDUCTASE ACTIVITY / TRINUCLEAR CLUSTER / DIOXYGEN REDUCTION | ||||||
Function / homology | ![]() bilirubin oxidase / laccase / sporulation resulting in formation of a cellular spore / outer membrane-bounded periplasmic space / oxidoreductase activity / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Silva, C.S. / Lindley, P.F. / Bento, I. | ||||||
![]() | ![]() Title: The Role of Asp116 in the Reductive Cleavage of Dioxygen to Water in Cota Laccase: Assistance During the Proton Transfer Mechanism Authors: Silva, C.S. / Damas, J.M. / Chen, Z. / Brissos, V. / Martins, L.O. / Soares, C.M. / Lindley, P.F. / Bento, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.7 KB | Display | ![]() |
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PDB format | ![]() | 96.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.2 KB | Display | ![]() |
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Full document | ![]() | 458.3 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a66C ![]() 4a67C ![]() 1w6lS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 58573.805 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 452 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-OH / | #4: Chemical | ChemComp-PER / | #5: Chemical | ChemComp-EPE / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDNonpolymer details | CU-O LINKAGE: CU4 BOUND TO HYDROXIDE ION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.69 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 8% PEG 6000 WITH 25% OF 2-METHYL-2,4-PENTANEDIOL (MPD) IN 0.1M HEPES BUFFER AT PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER PT135 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.544 Å / Relative weight: 1 |
Reflection | Resolution: 2→87.94 Å / Num. obs: 55571 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W6L Resolution: 2→87.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.672 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY SYSTEMATICALLY DISORDERED REGION BETWEEN RESIDUES 212 AND 215. LOOP REGION BETWEEN RESIDUES 89 AND 97 POORLY DEFINED.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.964 Å2
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Refinement step | Cycle: LAST / Resolution: 2→87.94 Å
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Refine LS restraints |
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