[English] 日本語
Yorodumi
- PDB-2xll: The crystal structure of bilirubin oxidase from Myrothecium verrucaria -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more