catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding Similarity search - Function
: / Catalase, four-helical domain / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site ...: / Catalase, four-helical domain / Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
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. 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. 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. 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.
Mass: 18.015 Da / Num. of mol.: 1682 / Source method: isolated from a natural source / Formula: H2O
Sequence details
GENBANK I52101. V123A MUTANT
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.2 Å3/Da / Density % sol: 44.13 % / Description: NONE
Crystal grow
pH: 5.2 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 5.2
Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9686 Å / Relative weight: 1
Reflection
Resolution: 1.93→29.41 Å / Num. obs: 202855 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shell
Resolution: 1.93→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 99.8
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Processing
Software
Name
Version
Classification
REFMAC
5.6.0117
refinement
XDS
datareduction
SCALA
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.93→29.41 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.383 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.14 / 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 IS ...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 IS NOT MODELLED DUE TO WEAK DENSITY. DISORDERED REGION BETWEEN RESIDUE 617 AND 622 IN CHAIN B IS NOT MODELLED DUE TO WEAK DENSITY. DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN C IS NOT MODELLED DUE TO WEAK DENSITY. DISORDERED REGION BETWEEN RESIDUE 649 AND 653 IN CHAIN C IS NOT MODELLED DUE TO WEAK DENSITY. DISORDERED REGION BETWEEN RESIDUE 618 AND 622 IN CHAIN D IS NOT MODELLED DUE TO WEAK DENSITY DISORDERED REGION BETWEEN RESIDUE 649 AND 653 IN CHAIN D IS NOT MODELLED DUE TO WEAK DENSITY. WATER MOLECULES F1077 AND F1078 PRESENT NEXT TO ARG127 IN CHAIN A HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F1531 AND F1558 PRESENT NEXT TO ARG127 IN CHAIN B HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F1634 AND F1635 PRESENT NEXT TO ARG127 IN CHAIN C HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F1519 AND F1636 PRESENT NEXT TO ARG127 IN CHAIN D HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F912, F1022, F1500, F1501, F1502 AND F1503 ARE PLACED SO THAT THE COMPLEXES FORMED WERE SIX COORDINATE FOR CA2 RESIDUE GLU672 PRESENT ON THE SURFACE IN CHAIN C WHICH HAS B FACTOR GREATER THAN 100 IS MODELLED FROM POOR DENSITY MAP
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19929
9910
4.9 %
RANDOM
Rwork
0.16576
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obs
0.16745
191147
97.7 %
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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