[English] 日本語
![](img/lk-miru.gif)
- PDB-4aum: Crystal structure, recombinant expression and mutagenesis studies... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4aum | ||||||
---|---|---|---|---|---|---|---|
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 |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 982.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 115 KB | Display | |
Data in CIF | ![]() | 175.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aueC ![]() 4aulC ![]() 4aunSC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: Protein | Mass: 79280.867 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HDD / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-1PE / | #5: Water | ChemComp-HOH / | Sequence details | GB I52101 | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % / Description: NONE |
---|---|
Crystal grow | pH: 5.4 Details: PROTEIN CRYSTAL WAS OBTAINED IN 6-16 % PEG400, 0.2 M POTASSIUM CHLORIDE, 0.01 M CALCIUM CHLORIDE DEHYDRATE AND 0.05 M SODIUM CACODYLATE TRIHYDRATE AT PH 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2011 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→29.32 Å / Num. obs: 506416 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.4 / % possible all: 94.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AUN Resolution: 1.4→113 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.494 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.048 / 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 617 AND 622 IN CHAIN A ...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 617 AND 622 IN CHAIN A WAS NOT MODELED DUE TO WEAK DENSITY C-TERMINAL RESIDUE SER698 IN CHAIN A WAS NOT MODELED DUE TO WEAK DENSITY. DISORDERED REGION BETWEEN RESIDUE 617 AND 622 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. DISORDERED REGION BETWEEN RESIDUE 649 AND 653 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 649 AND 653 IN CHAIN D WAS NOT MODELED DUE TO WEAK DENSITY. C-TERMINAL RESIDUE SER698 IN CHAIN D WAS NOT MODELED DUE TO WEAK DENSITY. WATER MOLECULES F2171, F2172 AND F2173 PRESENT NEXT TO ARG127 IN CHAIN A HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F2174, F2175 AND F2176 PRESENT NEXT TO ARG127 IN CHAIN B HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F2177, F2178 AND F2179 PRESENT NEXT TO ARG127 IN CHAIN C HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F2180, F2181 AND F2182 PRESENT NEXT TO ARG127 IN CHAIN D HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F986, F1083, F1105, F1144, F1193 AND F1916 WERE PLACED SO THAT THE COMPLEXES FORMED WERE SIX COORDINATE FOR CA1.RESIDUE GLU654 IN CHAINS C AND D ARE TRUNCATED DUE TO WEAK DENSITY FOR THEIR SIDECHAINS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.02 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→113 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|