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Basic information

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


catechol oxidase activity / 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 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
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesSCYTALIDIUM THERMOPHILUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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
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. 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. 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. 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.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,97420
Polymers317,0274
Non-polymers2,94716
Water44,9832497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54440 Å2
ΔGint-446.9 kcal/mol
Surface area72720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.958, 121.919, 124.919
Angle α, β, γ (deg.)90.00, 115.28, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99864, 0.05193, 0.0048), (0.05214, 0.99603, 0.07216), (-0.00103, 0.07231, -0.99738)127.75942, -1.25366, -56.09892
2given(0.98286, -0.04488, -0.17879), (-0.04486, -0.99898, 0.00416), (-0.1788, 0.00393, -0.98388)-4.15639, -15.26555, -45.02575
3given(-0.98419, -0.00644, 0.17697), (-0.00749, -0.99693, -0.07794), (0.17693, -0.07804, 0.98112)131.17493, -19.96002, -12.49931

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Components

#1: Protein
CATALASE-PHENOL OXIDASE


Mass: 79256.820 Da / Num. of mol.: 4
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: M4GGR6*PLUS, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2497 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE GENBANK ID I52101, MUTATION H82N RELATIVE TO THE GENBANK SEQUENCE.

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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: 2.18 Å3/Da / Density % sol: 43.64 % / Description: NONE
Crystal growpH: 5
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 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→29.01 Å / Num. obs: 417266 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.5→28.96 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.645 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE 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 ...Details: HYDROGENS HAVE BEEN ADDED IN THE 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. DISORDERED REGION BETWEEN RESIDUE 618 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 650 AND 653 IN CHAIN C WAS NOT MODELED DUE TO WEAK DENSITY. DISORDERED REGION BETWEEN RESIDUE 617 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. WATER MOLECULES F776, F2122 AND F2123 PRESENT NEXT TO ARG127 IN CHAIN A HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F1935, F2124 AND F2130 PRESENT NEXT TO ARG127 IN CHAIN B HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F667, F2125 AND F2126 PRESENT NEXT TO ARG127 IN CHAIN C HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F763, F1226, F2127 AND F2128 PRESENT NEXT TO ARG127 IN CHAIN D HAVE OCCUPANCY VALUES OF 0.5. WATER MOLECULES F1562, F1565, F1691, F1886, F1887 AND F1888 WERE PLACED SO THAT THE COMPLEXES FORMED WERE SIX COORDINATE FOR CA6.
RfactorNum. reflection% reflectionSelection details
Rfree0.19334 20735 5 %RANDOM
Rwork0.14296 ---
obs0.14547 395846 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å21.48 Å2
2---0.85 Å20 Å2
3---2.21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20990 0 184 2497 23671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222540
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.94830846
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36652898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98423.8641144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7153496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.80815175
X-RAY DIFFRACTIONr_chiral_restr0.1140.23277
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02118035
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_restr3.30722540
X-RAY DIFFRACTIONr_sphericity_free26.9795416
X-RAY DIFFRACTIONr_sphericity_bonded13.86723982
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 1535 -
Rwork0.25 29003 -
obs--96.86 %

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