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- PDB-5or3: Crystal structure of Aspergillus oryzae catechol oxidase in met/d... -

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Basic information

Entry
Database: PDB / ID: 5or3
TitleCrystal structure of Aspergillus oryzae catechol oxidase in met/deoxy-form
Componentscatechol oxidase
KeywordsOXIDOREDUCTASE / catechol oxidase / polyphenol oxidase / coupled 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 / CITRATE ANION / alpha-D-mannopyranose / PEROXIDE ION / Tyrosinase copper-binding domain-containing protein
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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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)174,91141
Polymers168,0994
Non-polymers6,81237
Water21,2041177
1
A: catechol oxidase
D: catechol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,36920
Polymers84,0502
Non-polymers3,31918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: catechol oxidase
C: catechol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,54321
Polymers84,0502
Non-polymers3,49319
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.627, 81.392, 82.200
Angle α, β, γ (deg.)87.19, 89.23, 73.89
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)
Gene: AO090001000383 / Production host: Trichoderma reesei RUT C-30 (fungus) / References: UniProt: Q2UNF9

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Sugars , 5 types, 19 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.: 2
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 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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
#6: Sugar
ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 5
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
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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

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Non-polymers , 5 types, 1195 molecules

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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C2H6O2
#9: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H5O7
#10: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1177 / 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: 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: Diamond / Beamline: I02 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→29.13 Å / Num. obs: 136838 / % possible obs: 97.1 % / Redundancy: 3.55 % / Rrim(I) all: 0.135 / Net I/σ(I): 7.37
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 1.26 / Num. unique all: 21443 / CC1/2: 0.601 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.795→29.123 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 6840 5 %
Rwork0.1759 --
obs0.1775 136809 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.795→29.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11529 0 415 1177 13121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612409
X-RAY DIFFRACTIONf_angle_d0.73516860
X-RAY DIFFRACTIONf_dihedral_angle_d11.4377224
X-RAY DIFFRACTIONf_chiral_restr0.0431853
X-RAY DIFFRACTIONf_plane_restr0.0042165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.795-1.81540.42020.38283845X-RAY DIFFRACTION85
1.8154-1.83680.34112280.31654322X-RAY DIFFRACTION97
1.8368-1.85920.30932220.29724226X-RAY DIFFRACTION96
1.8592-1.88270.34062280.29144320X-RAY DIFFRACTION96
1.8827-1.90750.30222280.26614335X-RAY DIFFRACTION97
1.9075-1.93360.28352270.24764308X-RAY DIFFRACTION97
1.9336-1.96120.24862270.24174316X-RAY DIFFRACTION97
1.9612-1.99050.2882260.23334306X-RAY DIFFRACTION97
1.9905-2.02160.24832300.22844354X-RAY DIFFRACTION97
2.0216-2.05470.24632260.21914305X-RAY DIFFRACTION97
2.0547-2.09010.25392300.21464368X-RAY DIFFRACTION97
2.0901-2.12810.24452250.20674272X-RAY DIFFRACTION97
2.1281-2.16910.22132300.19344366X-RAY DIFFRACTION97
2.1691-2.21330.21442280.18824330X-RAY DIFFRACTION98
2.2133-2.26140.22172290.18974358X-RAY DIFFRACTION97
2.2614-2.3140.24492280.17884322X-RAY DIFFRACTION97
2.314-2.37190.22192290.1754356X-RAY DIFFRACTION98
2.3719-2.4360.22222310.17244382X-RAY DIFFRACTION98
2.436-2.50760.22172310.16794388X-RAY DIFFRACTION98
2.5076-2.58850.22572280.15974333X-RAY DIFFRACTION98
2.5885-2.68090.1792300.15574374X-RAY DIFFRACTION98
2.6809-2.78820.19542310.1624399X-RAY DIFFRACTION98
2.7882-2.9150.20672320.16394403X-RAY DIFFRACTION98
2.915-3.06850.2012290.16484350X-RAY DIFFRACTION98
3.0685-3.26050.18942330.15974423X-RAY DIFFRACTION98
3.2605-3.51190.18392290.15884351X-RAY DIFFRACTION99
3.5119-3.86460.17132310.14444397X-RAY DIFFRACTION98
3.8646-4.42210.14642300.13184382X-RAY DIFFRACTION98
4.4221-5.5650.16132320.13394398X-RAY DIFFRACTION98
5.565-29.12680.19292300.1844380X-RAY DIFFRACTION98

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