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- PDB-5e9n: Steccherinum murashkinskyi laccase at 0.95 resolution -

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Basic information

Entry
Database: PDB / ID: 5e9n
TitleSteccherinum murashkinskyi laccase at 0.95 resolution
ComponentsLaccase 2
KeywordsOXIDOREDUCTASE / laccase / enzyme
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding / extracellular region
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, type 1 / 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 / Chem-PG6 / Laccase 2
Similarity search - Component
Biological speciesSteccherinum murashkinskyi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsPolyakov, K.M. / Glazunova, O.A. / Fedorova, T.V. / Koroleva, O.V.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Structure-function study of two new middle-redox potential laccases from basidiomycetes Antrodiella faginea and Steccherinum murashkinskyi.
Authors: Glazunova, O.A. / Polyakov, K.M. / Moiseenko, K.V. / Kurzeev, S.A. / Fedorova, T.V.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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.id / _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_alt_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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Laccase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,30710
Polymers56,6481
Non-polymers1,6599
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-5 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.510, 83.270, 111.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Laccase 2


Mass: 56648.480 Da / Num. of mol.: 1 / Fragment: UNP residues 20-546 / Source method: isolated from a natural source / Source: (natural) Steccherinum murashkinskyi (fungus) / References: UniProt: I1VE66, laccase
#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.: 2
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

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Non-polymers , 4 types, 738 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 0.2 ammoniun sulphate, 25% PEG 3350
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 0.95→8 Å / Num. obs: 981844 / % possible obs: 94.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.44
Reflection shellResolution: 0.95→1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FPX

3fpx


Resolution: 0.95→8 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.635 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.13941 15916 5 %RANDOM
Rwork0.12117 ---
obs0.12209 301501 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.028 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2---0.09 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 0.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 74 731 4544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194010
X-RAY DIFFRACTIONr_bond_other_d0.0010.023309
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.955493
X-RAY DIFFRACTIONr_angle_other_deg0.9137620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8965496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73225.189185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99315539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.261513
X-RAY DIFFRACTIONr_chiral_restr0.1310.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1441986
X-RAY DIFFRACTIONr_mcbond_other1.1141981
X-RAY DIFFRACTIONr_mcangle_it1.552482
X-RAY DIFFRACTIONr_mcangle_other1.4982478
X-RAY DIFFRACTIONr_scbond_it1.9132024
X-RAY DIFFRACTIONr_scbond_other1.7981999
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2952982
X-RAY DIFFRACTIONr_long_range_B_refined3.445528
X-RAY DIFFRACTIONr_long_range_B_other2.8555011
X-RAY DIFFRACTIONr_rigid_bond_restr5.38733882
X-RAY DIFFRACTIONr_sphericity_free26.915582
X-RAY DIFFRACTIONr_sphericity_bonded9.68254254
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 1097 -
Rwork0.277 21636 -
obs--96.08 %

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