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- PDB-4b2y: Probing the active center of catalase-phenol oxidase from Scytali... -

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Basic information

Entry
Database: PDB / ID: 4b2y
TitleProbing the active center of catalase-phenol oxidase from Scytalidium thermophilum
ComponentsCATALASE-PHENOL OXIDASE
KeywordsOXIDOREDUCTASE / MOLECULAR CHANNELS / OXIDATIVE ACTIVITY
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol
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 immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / 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: 1.9 Å
AuthorsYuzugullu, Y. / Trinh, C.H. / Pearson, A.R. / Ogel, Z.B. / McPherson, M.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Investigating the Active Centre of the Scytalidium Thermophilum Catalase
Authors: Yuzugullu, Y. / Trinh, C.H. / Fairhurst, L. / Ogel, Z.B. / McPherson, M.J. / Pearson, A.R.
History
DepositionJul 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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. 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.

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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)319,84614
Polymers317,1404
Non-polymers2,70610
Water32,4991804
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53930 Å2
ΔGint-373.7 kcal/mol
Surface area73570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.323, 121.205, 124.965
Angle α, β, γ (deg.)90.00, 115.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99882, 0.04839, 0.00378), (0.04854, 0.99641, 0.06932), (-0.00041, 0.06943, -0.99759)127.79439, -1.14769, -55.99645
2given(0.98282, -0.04198, -0.17971), (-0.04195, -0.99911, 0.00396), (-0.17971, 0.00365, -0.98371)-4.35447, -15.37916, -44.77952
3given(-0.98389, -0.00669, 0.17866), (-0.00665, -0.99724, -0.07394), (0.17866, -0.07394, 0.98113)131.28563, -19.82051, -12.57037

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Components

#1: Protein
CATALASE-PHENOL OXIDASE


Mass: 79284.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COVALENT BOND CYS123 TO HIS83 CE1 / 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: R4GRT6*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.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1804 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATION VAL 123 TO CYS

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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: 2.17 Å3/Da / Density % sol: 43.29 % / Description: NONE
Crystal growpH: 5.6
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 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.9→29.26 Å / Num. obs: 209169 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.9→29.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.704 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.122 / 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 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 618 AND 622 IN CHAIN A IS NOT MODELLED DUE 622 IN CHAIN B IS NOT MODELLED DUE TO WEAK DENSITY 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 F1478 AND F1547 PRESENT NEXT TO ARG127 IN CHAIN A HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1243, F1428 AND F1644 PRESENT NEXT TO ARG127 IN CHAIN B HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F793, F1445 AND F1655 PRESENT NEXT TO ARG127 IN CHAIN C HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F1004 AND F1429 PRESENT NEXT TO ARG127 IN CHAIN D HAVE OCCUPANCY VALUES OF 0.5 WATER MOLECULES F987, F1124, F1232, F1233, F1234 AND F1235 WERE PLACED SO THAT THE COMPLEXES FORMED WERE SIX COORDINATE FOR CA1
RfactorNum. reflection% reflectionSelection details
Rfree0.18115 10347 4.9 %RANDOM
Rwork0.15016 ---
obs0.15172 198819 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å21.38 Å2
2---0.34 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21008 0 178 1804 22990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222556
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.94630881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05552904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54223.8791160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.167153503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.02715173
X-RAY DIFFRACTIONr_chiral_restr0.1030.23273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118045
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 751 -
Rwork0.202 14554 -
obs--99.38 %

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