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Basic information

Entry
Database: PDB / ID: 3abg
TitleX-ray Crystal Analysis of Bilirubin Oxidase from Myrothecium verrucaria at 2.3 angstrom Resolution using a Twin Crystal
ComponentsBilirubin oxidase
KeywordsOXIDOREDUCTASE / Bilirubin Oxidase / Cleavage on pair of basic residues / Glycoprotein / Metal-binding
Function / homology
Function and homology information


bilirubin oxidase activity / bilirubin oxidase / copper ion binding
Similarity search - Function
Multicopper oxidase / Multicopper oxidase, C-terminal / 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 / OXYGEN MOLECULE / Bilirubin oxidase
Similarity search - Component
Biological speciesAlbifimbria verrucaria (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMizutani, K. / Toyoda, M. / Sagara, K. / Takahashi, N. / Sato, A. / Kamitaka, Y. / Tsujimura, S. / Nakanishi, Y. / Sugiura, T. / Yamaguchi, S. ...Mizutani, K. / Toyoda, M. / Sagara, K. / Takahashi, N. / Sato, A. / Kamitaka, Y. / Tsujimura, S. / Nakanishi, Y. / Sugiura, T. / Yamaguchi, S. / Kano, K. / Mikami, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: X-ray analysis of bilirubin oxidase from Myrothecium verrucaria at 2.3 A resolution using a twinned crystal
Authors: Mizutani, K. / Toyoda, M. / Sagara, K. / Takahashi, N. / Sato, A. / Kamitaka, Y. / Tsujimura, S. / Nakanishi, Y. / Sugiura, T. / Yamaguchi, S. / Kano, K. / Mikami, B.
History
DepositionDec 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_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 3.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / database_2 / database_PDB_caveat / diffrn / entity / entity_src_nat / pdbx_audit_support / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_contact_author / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _pdbx_database_status.SG_entry / _pdbx_entry_details.has_ligand_of_interest / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_R_free / _refine.occupancy_max / _refine.occupancy_min / _refine.overall_FOM_work_R_set / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.number_all / _reflns.pdbx_netI_over_sigmaI / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_diffrn_id / _software.classification / _software.name / _software.version / _struct_ref.db_code / _struct_sheet.id / _struct_sheet.number_strands / _symmetry.space_group_name_Hall

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,67524
Polymers120,0192
Non-polymers3,65522
Water2,918162
1
A: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,67512
Polymers60,0101
Non-polymers1,66611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-19 kcal/mol
Surface area19170 Å2
MethodPISA
2
B: Bilirubin oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,99912
Polymers60,0101
Non-polymers1,99011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-9 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.742, 139.742, 135.561
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bilirubin oxidase /


Mass: 60009.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Albifimbria verrucaria (fungus) / References: UniProt: Q12737, bilirubin oxidase

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Sugars , 3 types, 4 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-ROHGlycam 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
[][D-1-deoxy-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-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: 910.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 180 molecules

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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer detailsBECAUSE TWINNED REFINEMENT CAN GIVE ARTIFICIALLY LOW R-VALUES, PARTS OF THE DEPOSITED STRUCTURE MAY ...BECAUSE TWINNED REFINEMENT CAN GIVE ARTIFICIALLY LOW R-VALUES, PARTS OF THE DEPOSITED STRUCTURE MAY NOT BE FREE OF SIGNIFICANT ERRORS

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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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% 2-methyl-2,4-pentanediol(MPD), 1.44M ammonium sulfate, 10% glycerol, 0.5M KCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2006
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.487
ReflectionResolution: 2.3→50 Å / Num. obs: 66384 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 30.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6514 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data collection
SOLVEphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→33.56 Å / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 22.4394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 3318 5.14 %RANDOM
Rwork0.158 61225 --
obs0.1729 64543 96.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8454 0 216 162 8832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01078932
X-RAY DIFFRACTIONf_angle_d1.037712200
X-RAY DIFFRACTIONf_chiral_restr0.0641328
X-RAY DIFFRACTIONf_plane_restr0.00821596
X-RAY DIFFRACTIONf_dihedral_angle_d16.87773224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.30861540.28262698X-RAY DIFFRACTION81.07
2.34-2.380.32291350.27532847X-RAY DIFFRACTION86.56
2.38-2.430.30491550.25752897X-RAY DIFFRACTION86.87
2.43-2.480.27021570.25072982X-RAY DIFFRACTION89.25
2.48-2.530.3211560.24682978X-RAY DIFFRACTION89.94
2.53-2.590.28541360.23443043X-RAY DIFFRACTION90.78
2.59-2.650.26451660.24133008X-RAY DIFFRACTION91.18
2.65-2.730.28131880.22673064X-RAY DIFFRACTION92.07
2.73-2.810.24971830.2143063X-RAY DIFFRACTION91.76
2.81-2.90.25781580.20713113X-RAY DIFFRACTION93.68
2.9-30.21981600.21173133X-RAY DIFFRACTION94.11
3-3.120.19782020.19633094X-RAY DIFFRACTION93.19
3.12-3.260.19771490.18873180X-RAY DIFFRACTION95.18
3.26-3.430.21051680.18943153X-RAY DIFFRACTION94.54
3.43-3.650.18151640.17123165X-RAY DIFFRACTION94.9
3.65-3.930.1791710.15513162X-RAY DIFFRACTION94.61
3.93-4.320.171860.13643167X-RAY DIFFRACTION94.45
4.32-4.950.14261600.1213167X-RAY DIFFRACTION94.85
4.95-6.220.14141490.12153200X-RAY DIFFRACTION94.93
6.23-33.560.15411660.14563166X-RAY DIFFRACTION92.82

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