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- PDB-2xll: The crystal structure of bilirubin oxidase from Myrothecium verrucaria -

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Basic information

Entry
Database: PDB / ID: 2xll
TitleThe crystal structure of bilirubin oxidase from Myrothecium verrucaria
ComponentsBILIRUBIN OXIDASE
KeywordsOXIDOREDUCTASE / BLUE MULTICOPPER OXIDASE / LACCASE / ASCOMYCETE / DIOXYGEN REDUCTION / HEME CATABOLISM / GLYCOPROTEIN / PROTEIN FILM VOLTAMMETRY
Function / homology
Function and homology information


bilirubin oxidase activity / bilirubin oxidase / copper ion binding
Similarity search - Function
Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Bilirubin oxidase
Similarity search - Component
Biological speciesMYROTHECIUM VERRUCARIA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å
AuthorsMcNamara, T.P. / Lowe, E.D. / Cracknell, J.A. / Blanford, C.F.
CitationJournal: Dalton Trans / Year: 2011
Title: Bilirubin Oxidase from Myrothecium Verrucaria: X- Ray Determination of the Complete Crystal Structure and a Rational Surface Modification for Enhanced Electrocatalytic O(2) Reduction.
Authors: Cracknell, J.A. / Mcnamara, T.P. / Lowe, E.D. / Blanford, C.F.
History
DepositionJul 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / 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.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _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_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_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.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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 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: BILIRUBIN OXIDASE
B: BILIRUBIN OXIDASE
C: BILIRUBIN OXIDASE
D: BILIRUBIN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,45128
Polymers240,0394
Non-polymers4,41224
Water23,6901315
1
A: BILIRUBIN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1137
Polymers60,0101
Non-polymers1,1036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BILIRUBIN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1137
Polymers60,0101
Non-polymers1,1036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BILIRUBIN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1137
Polymers60,0101
Non-polymers1,1036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BILIRUBIN OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1137
Polymers60,0101
Non-polymers1,1036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.793, 83.602, 143.148
Angle α, β, γ (deg.)89.98, 89.89, 89.90
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:533 )
211CHAIN B AND (RESSEQ 1:533 )
311CHAIN C AND (RESSEQ 1:533 )
411CHAIN D AND (RESSEQ 1:533 )

NCS oper:
IDCodeMatrixVector
1given(-1, 0.00196, -0.00095), (0.00196, 1, -4.0E-5), (0.00095, -4.0E-5, -1)-2.12062, -41.81276, 71.48102
2given(1, -0.00187, -0.00073), (-0.00187, -1, -0.0002), (-0.00073, 0.00021, -1)0.01208, 84.39784, -0.09409
3given(-1, -0.00013, 0.00194), (0.00013, -1, -0.0001), (0.00194, -0.0001, 1)-2.25374, 42.57363, -71.59449

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Components

#1: Protein
BILIRUBIN OXIDASE


Mass: 60009.688 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) MYROTHECIUM VERRUCARIA (fungus) / References: UniProt: Q12737, bilirubin oxidase
#2: 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.: 8
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
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1315 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.1 % / Description: NONE
Crystal growpH: 8.7
Details: 0.1 M CAPS, 1.23 M NAH2PO4 / NA2HPO4, 0.2 M LI2SO4, PH 8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2010
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.31→29.8 Å / Num. obs: 96851 / % possible obs: 89.7 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.3
Reflection shellResolution: 2.31→2.43 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 5.5 / % possible all: 58.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSK

1gsk


Resolution: 2.305→29.801 Å / SU ML: 0.28 / σ(F): 0.02 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 4635 5 %
Rwork0.1697 --
obs0.172 93296 86.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.05 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 18.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.6395 Å20.0617 Å2-0.042 Å2
2---2.5012 Å20.7293 Å2
3---1.8616 Å2
Refinement stepCycle: LAST / Resolution: 2.305→29.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16808 0 240 1315 18363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817696
X-RAY DIFFRACTIONf_angle_d1.12824216
X-RAY DIFFRACTIONf_dihedral_angle_d14.2786356
X-RAY DIFFRACTIONf_chiral_restr0.0782608
X-RAY DIFFRACTIONf_plane_restr0.0063184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4233X-RAY DIFFRACTIONPOSITIONAL
12B4233X-RAY DIFFRACTIONPOSITIONAL0.022
13C4233X-RAY DIFFRACTIONPOSITIONAL0.025
14D4233X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3052-2.38760.23212690.15955349X-RAY DIFFRACTION52
2.3876-2.48310.25623390.16567090X-RAY DIFFRACTION69
2.4831-2.59610.22854950.15339459X-RAY DIFFRACTION92
2.5961-2.73290.23174880.16019505X-RAY DIFFRACTION93
2.7329-2.90390.22685190.16429751X-RAY DIFFRACTION95
2.9039-3.12790.21285040.16799835X-RAY DIFFRACTION96
3.1279-3.44230.22065260.17659725X-RAY DIFFRACTION95
3.4423-3.93940.25214310.22528290X-RAY DIFFRACTION81
3.9394-4.95960.15085060.11629719X-RAY DIFFRACTION95
4.9596-29.8030.17865580.14489938X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06250.0317-0.03070.1238-0.07820.05520.01120.0022-0.0015-0.0136-0.01770.01860.00440.0032-0.00480.0115-0.0011-0.00380.02850.0096-0.001611.825534.961828.7293
20.0944-0.0287-0.01510.09740.00380.02560.0062-0.0002-0.00390.0215-0.0274-0.013-0.0178-0.00150.01070.0177-0.0014-0.00550.03170.00210.005-13.9049-6.828542.7618
30.0346-0.0240.01940.0977-0.02530.0914-0.0053-0.0173-0.00760.002-0.00350.02010.0125-0.0067-0.02390.00860.0008-0.0030.03150.00940.009411.749849.4085-28.8249
40.07990.03820.03530.0801-0.00240.046-0.00280.01220.0003-0.0167-0.0157-0.00680.00940.01520.00220.0055-0.0003-0.00420.03130.00630.0046-14.02697.6105-42.8452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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