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- PDB-5or4: Crystal structure of Aspergillus oryzae catechol oxidase in deoxy-form -

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Basic information

Entry
Database: PDB / ID: 5or4
TitleCrystal structure of Aspergillus oryzae catechol oxidase in deoxy-form
Componentscatechol oxidase
KeywordsOXIDOREDUCTASE / catechol oxidase / polyphenol oxidase / binuclear copper enzyme / type 3 copper center
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 / Tyrosinase copper-binding domain-containing protein
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.445 Å
AuthorsHakulinen, N. / Penttinen, L. / Rutanen, C. / Rouvinen, J.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland256937 Finland
Academy of Finland292705 Finland
CitationJournal: PLoS ONE / Year: 2018
Title: A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.
Authors: Penttinen, L. / Rutanen, C. / Saloheimo, M. / Kruus, K. / Rouvinen, J. / Hakulinen, N.
History
DepositionAug 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
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 / 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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_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 2.1Jan 17, 2024Group: 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
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: catechol oxidase
B: catechol oxidase
C: catechol oxidase
D: catechol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,76630
Polymers168,0994
Non-polymers5,66626
Water8,341463
1
A: catechol oxidase
D: catechol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,78115
Polymers84,0502
Non-polymers2,73113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: catechol oxidase
C: catechol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,98415
Polymers84,0502
Non-polymers2,93513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.856, 81.879, 82.705
Angle α, β, γ (deg.)87.15, 89.04, 73.86
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
catechol oxidase


Mass: 42024.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (strain ATCC 42149 / RIB 40) (mold)
Strain: ATCC 42149 / RIB 40 / Gene: AO090001000383 / Production host: Trichoderma reesei RUT C-30 (fungus) / References: UniProt: Q2UNF9

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Sugars , 4 types, 18 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.: 3
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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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.: 11
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.: 3
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 , 2 types, 471 molecules

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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 6 % ethylene glycol, 10 % PEG 20000, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 53530 / % possible obs: 92.2 % / Redundancy: 1.76 % / Rrim(I) all: 0.202 / Net I/σ(I): 6.19
Reflection shellResolution: 2.43→2.57 Å / Mean I/σ(I) obs: 1.78 / Num. unique all: 7542 / CC1/2: 0.47 / Rrim(I) all: 0.763 / % possible all: 80.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J3P

4j3p


Resolution: 2.445→47.785 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 2674 5 %
Rwork0.2028 --
obs0.2058 53462 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.445→47.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11517 0 340 463 12320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612221
X-RAY DIFFRACTIONf_angle_d0.69116667
X-RAY DIFFRACTIONf_dihedral_angle_d5.437058
X-RAY DIFFRACTIONf_chiral_restr0.0441844
X-RAY DIFFRACTIONf_plane_restr0.0042145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4449-2.48940.35561350.29152562X-RAY DIFFRACTION90
2.4894-2.53730.34811430.2742723X-RAY DIFFRACTION95
2.5373-2.5890.31281410.25272672X-RAY DIFFRACTION95
2.589-2.64530.33591440.23852734X-RAY DIFFRACTION96
2.6453-2.70690.32231390.22992649X-RAY DIFFRACTION95
2.7069-2.77460.28051440.23042732X-RAY DIFFRACTION96
2.7746-2.84960.26261390.2272650X-RAY DIFFRACTION94
2.8496-2.93340.32311450.23632741X-RAY DIFFRACTION96
2.9334-3.02810.27921440.2242733X-RAY DIFFRACTION96
3.0281-3.13630.29221400.22232661X-RAY DIFFRACTION95
3.1363-3.26180.26181400.2152669X-RAY DIFFRACTION95
3.2618-3.41020.30161430.21442724X-RAY DIFFRACTION95
3.4102-3.590.28251410.20752669X-RAY DIFFRACTION94
3.59-3.81480.24551390.19792648X-RAY DIFFRACTION94
3.8148-4.10920.22491410.17092668X-RAY DIFFRACTION94
4.1092-4.52240.2271370.15822604X-RAY DIFFRACTION93
4.5224-5.17620.20291390.15562639X-RAY DIFFRACTION93
5.1762-6.51880.22191400.17762659X-RAY DIFFRACTION95
6.5188-47.79450.17111400.17212651X-RAY DIFFRACTION93

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