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Open data
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Basic information
Entry | Database: PDB / ID: 6nt1 | ||||||
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Title | Catalase 3 from N.Crassa in ferrous state (2.89 MGy) | ||||||
![]() | Catalase-3 | ||||||
![]() | OXIDOREDUCTASE / X-ray reduced / Heme / ferrous Catalase | ||||||
Function / homology | ![]() catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Zarate-Romero, A. / Rudino-Pinera, E. / Stojanoff, V. | ||||||
![]() | ![]() Title: X-ray driven reduction of Cpd I of Catalase-3 from N. crassa reveals differential sensitivity of active sites and formation of ferrous state. Authors: Zarate-Romero, A. / Stojanoff, V. / Cohen, A.E. / Hansberg, W. / Rudino-Pinera, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 590.4 KB | Display | ![]() |
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PDB format | ![]() | 479.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 115.1 KB | Display | |
Data in CIF | ![]() | 169.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aj9SC ![]() 6nswC ![]() 6nsyC ![]() 6nszC ![]() 6nt0C S: Starting model for refinement C: citing same article ( |
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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, 4 molecules ABCD
#1: Protein | Mass: 79322.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 Gene: cat-3, NCU00355 / Plasmid: pCold I / Production host: ![]() ![]() |
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-Non-polymers , 9 types, 2047 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-PGE / #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-EOH / #8: Chemical | ChemComp-P6G / | #9: Chemical | ChemComp-PG4 / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.32 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.6 / Details: Ammonium tartrate dibasic, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 29, 2012 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9674 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.655 Å / Num. obs: 159994 / % possible obs: 96.6 % / Redundancy: 3.15 % / Biso Wilson estimate: 14.92 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.177 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.21 / Num. unique obs: 11710 / CC1/2: 0.806 / Rrim(I) all: 0.441 / % possible all: 80.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4AJ9 Resolution: 2.2→29.655 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.97 Å2 / Biso mean: 16.8862 Å2 / Biso min: 3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→29.655 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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