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- PDB-4aun: Crystal structure, recombinant expression and mutagenesis studies... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4aun | ||||||
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Title | Crystal structure, recombinant expression and mutagenesis studies of the bifunctional catalase-phenol oxidase from Scytalidium thermophilum | ||||||
![]() | CATALASE-PHENOL OXIDASE | ||||||
![]() | OXIDOREDUCTASE / CATALASE / PHENOL OXIDASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Yuzugullu, Y. / Trinh, C.H. / Smith, M.A. / Pearson, A.R. / Phillips, S.E.V. / Sutay Kocabas, D. / Bakir, U. / Ogel, Z.B. / McPherson, M.J. | ||||||
![]() | ![]() Title: Structure, Recombinant Expression and Mutagenesis Studies of the Catalase with Oxidase Activity from Scytalidium Thermophilum Authors: Yuzugullu, Y. / Trinh, C.H. / Smith, M.A. / Pearson, A.R. / Phillips, S.E.V. / Sutay Kocabas, D. / Bakir, U. / Ogel, Z.B. / McPherson, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 915.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 211.1 KB | Display | |
Data in CIF | ![]() | 304.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aueC ![]() 4aulSC ![]() 4aumC 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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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 79328.906 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HDD / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Sequence details | VAL 123 PHE MUTATION RELATIVE TO GENBANK SEQUENCE GENBANK ID I52101 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.2 % |
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Crystal grow | pH: 5 Details: PROTEIN CRYSTAL WAS OBTAINED IN 8-18% PEG 4000, 0.2 M POTASSIUM CHLORIDE, 0.01 M CALCIUM CHLORIDE DEHYDRATE AND 0.05 M SODIUM CACODYLATE TRIHYDRATE AT PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2011 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9464 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.89 Å / Num. obs: 409557 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AUL Resolution: 1.92→69.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.111 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN A WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN A WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 649 AND 653 IN CHAIN A WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN B WAS NOT MODELED DUE TO WEAK DENSITY C-TERMINAL RESIDUE SER698 IN CHAIN B WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN C WAS NOT MODELED DUE TO WEAK DENSITY C-TERMINAL RESIDUE SER698 IN CHAIN C WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN D WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN E WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 649 AND 655 IN CHAIN E WAS NOT MODELED DUE TO WEAK DENSITY C-TERMINAL RESIDUE SER698 IN CHAIN E WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN F WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 649 AND 655 IN CHAIN F WAS NOT MODELED DUE TO WEAK DENSITY C-TERMINAL RESIDUE SER698 IN CHAIN F WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN G WAS NOT MODELED DUE TO WEAK DENSITY C-TERMINAL RESIDUE SER698 IN CHAIN G WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN H WAS NOT MODELED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 650 AND 655 IN CHAIN H WAS NOT MODELED DUE TO WEAK DENSITY WATER MOLECULES F1408 AND F1409 PRESENT NEXT TO ARG127 IN CHAIN A HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1410 AND F1520 PRESENT NEXT TO ARG127 IN CHAIN B HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1418 AND F1420 PRESENT NEXT TO ARG127 IN CHAIN C HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1478, F2237, F3071 AND F3089 PRESENT NEXT TO ARG127 IN CHAIN D HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1417 AND F1450 PRESENT NEXT TO ARG127 IN CHAIN E HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1467 AND F1468 PRESENT NEXT TO ARG127 IN CHAIN F HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1484 AND F2251 PRESENT NEXT TO ARG127 IN CHAIN G HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1488 AND F1490 PRESENT NEXT TO ARG127 IN CHAIN H HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1325, F1326, F1327, F1328, F1329 AND F1330 WERE PLACED SO THAT THE COMPLEXES FORMED WERE SIX COORDINATE FOR CA1
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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 mean: 15.535 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→69.94 Å
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Refine LS restraints |
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