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Basic information

Entry
Database: PDB / ID: 4aun
TitleCrystal structure, recombinant expression and mutagenesis studies of the bifunctional catalase-phenol oxidase from Scytalidium thermophilum
ComponentsCATALASE-PHENOL OXIDASE
KeywordsOXIDOREDUCTASE / CATALASE / PHENOL OXIDASE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / 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, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / 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
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Catalase
Similarity search - Component
Biological speciesSCYTALIDIUM THERMOPHILUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsYuzugullu, 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.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
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
DepositionMay 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALASE-PHENOL OXIDASE
B: CATALASE-PHENOL OXIDASE
C: CATALASE-PHENOL OXIDASE
D: CATALASE-PHENOL OXIDASE
E: CATALASE-PHENOL OXIDASE
F: CATALASE-PHENOL OXIDASE
G: CATALASE-PHENOL OXIDASE
H: CATALASE-PHENOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)640,05225
Polymers634,6318
Non-polymers5,42117
Water61,3413405
1
A: CATALASE-PHENOL OXIDASE
B: CATALASE-PHENOL OXIDASE
G: CATALASE-PHENOL OXIDASE
H: CATALASE-PHENOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,04613
Polymers317,3164
Non-polymers2,7309
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53690 Å2
ΔGint-353.6 kcal/mol
Surface area73090 Å2
MethodPISA
2
C: CATALASE-PHENOL OXIDASE
E: CATALASE-PHENOL OXIDASE
hetero molecules

C: CATALASE-PHENOL OXIDASE
E: CATALASE-PHENOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,00612
Polymers317,3164
Non-polymers2,6908
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area53730 Å2
ΔGint-349.2 kcal/mol
Surface area72690 Å2
MethodPISA
3
D: CATALASE-PHENOL OXIDASE
F: CATALASE-PHENOL OXIDASE
hetero molecules

D: CATALASE-PHENOL OXIDASE
F: CATALASE-PHENOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,00612
Polymers317,3164
Non-polymers2,6908
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area53670 Å2
ΔGint-351.3 kcal/mol
Surface area72740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.370, 243.290, 97.060
Angle α, β, γ (deg.)90.00, 104.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2402-

HOH

21C-2295-

HOH

31E-2216-

HOH

41F-2248-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.51398, -0.03672, 0.85702), (-0.03525, -0.99734, -0.06387), (0.85708, -0.06304, 0.51131)98.05022, 136.25128, -49.86272
3given(0.48096, 0.03747, -0.87594), (0.0003, -0.99909, -0.04258), (-0.87675, 0.02022, -0.48053)-32.7585, 73.39867, 54.18376
4given(-0.54713, -0.03542, 0.8363), (0.00056, -0.99912, -0.04195), (0.83705, -0.02249, 0.54667)139.75682, 73.13268, 42.57291
5given(-0.99931, 0.00094, -0.03726), (-0.00063, 0.99911, 0.04214), (0.03727, 0.04214, -0.99842)63.1577, -60.62431, -4.97986
6given(0.99918, 0.00174, -0.04042), (2.0E-5, 0.99906, 0.04339), (0.04046, -0.04335, 0.99824)39.63706, -60.91383, 94.27133
7given(0.51188, 0.03753, -0.85824), (0.03627, -0.9991, -0.02205), (-0.85829, -0.01984, -0.51278)28.51448, 131.82472, 55.90357
8given(-1, -0.00139, -0.00143), (-0.0015, 0.99644, 0.08426), (0.00131, 0.08426, -0.99644)126.57835, 0.33295, -5.33403

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Components

#1: Protein
CATALASE-PHENOL OXIDASE


Mass: 79328.906 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCYTALIDIUM THERMOPHILUM (fungus) / Plasmid: PETCATPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: M4GGR8*PLUS, catalase
#2: Chemical
ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


Mass: 632.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O5
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3405 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsVAL 123 PHE MUTATION RELATIVE TO GENBANK SEQUENCE GENBANK ID I52101

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.2 %
Crystal growpH: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9464
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AUL

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
RfactorNum. reflection% reflectionSelection details
Rfree0.20054 21640 5 %RANDOM
Rwork0.16422 ---
obs0.16605 409557 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.535 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0.95 Å2
2---0.57 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.92→69.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41944 0 361 3405 45710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0244416
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.94860735
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55555625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15423.8582260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.351156803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.99115334
X-RAY DIFFRACTIONr_chiral_restr0.080.26477
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02135382
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.918→1.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 1506 -
Rwork0.246 30193 -
obs--99.96 %

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