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- PDB-4j3p: Crystal structure of full-length catechol oxidase from Aspergillu... -

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Basic information

Entry
Database: PDB / ID: 4j3p
TitleCrystal structure of full-length catechol oxidase from Aspergillus oryzae
ComponentsCatechol oxidase
KeywordsOXIDOREDUCTASE / catechol oxidase / type-3 copper center / binuclear copper enzyme / glycosylated
Function / homology
Function and homology information


catechol oxidase activity / metal ion binding
Similarity search - Function
di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Common central domain of tyrosinase / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / alpha-D-mannopyranose / OXYGEN MOLECULE / Tyrosinase copper-binding domain-containing protein
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 2.5 Å
AuthorsHakulinen, N. / Gasparetti, C. / Kaljunen, H. / Rouvinen, J.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2013
Title: The crystal structure of an extracellular catechol oxidase from the ascomycete fungus Aspergillus oryzae.
Authors: Hakulinen, N. / Gasparetti, C. / Kaljunen, H. / Kruus, K. / Rouvinen, J.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,71010
Polymers42,0251
Non-polymers1,6859
Water4,558253
1
A: Catechol oxidase
hetero molecules

A: Catechol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,42120
Polymers84,0502
Non-polymers3,37118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1730 Å2
ΔGint-14 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.880, 118.880, 84.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2344-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol oxidase


Mass: 42024.855 Da / Num. of mol.: 1 / Fragment: UNP residues 26-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Strain: VTT-D-88348 / Gene: 5990879 / Plasmid: pGF007 / Production host: Trichoderma reesei (fungus) / Strain (production host): RutC-30 / References: UniProt: Q2UNF9, catechol oxidase

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Sugars , 3 types, 5 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 257 molecules

#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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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: 4.1 Å3/Da / Density % sol: 70.01 %
Crystal growTemperature: 294 K / pH: 4.5
Details: 1.7 M ammonium sulfate, 5% glycerol and 0.1 M sodium acetate at pH 4.5., VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2009
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 22817 / % possible obs: 93.5 % / Rsym value: 5.1 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 4.4 / Rsym value: 0.288 / % possible all: 95.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD, molecular replacement
Starting model: PDB ENTRY 1WX2

1wx2


Resolution: 2.5→19.54 Å / SU ML: 0.26 / σ(F): 1.99 / Phase error: 26.02 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.245 1141 5 %
Rwork0.188 --
obs0.191 22804 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 101 253 3235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183076
X-RAY DIFFRACTIONf_angle_d1.084200
X-RAY DIFFRACTIONf_dihedral_angle_d16.7261115
X-RAY DIFFRACTIONf_chiral_restr0.069461
X-RAY DIFFRACTIONf_plane_restr0.005533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61360.28951440.21082730X-RAY DIFFRACTION96
2.6136-2.75110.28171440.2112732X-RAY DIFFRACTION96
2.7511-2.92290.27421430.21182712X-RAY DIFFRACTION96
2.9229-3.14770.2931420.20342712X-RAY DIFFRACTION96
3.1477-3.46290.2681420.19182701X-RAY DIFFRACTION95
3.4629-3.96040.21711400.16692655X-RAY DIFFRACTION93
3.9604-4.9760.18931420.15692686X-RAY DIFFRACTION93
4.976-19.54190.24961440.20272735X-RAY DIFFRACTION92

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