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Entry
Database: PDB / ID: 5a7e
TitleCrystallographic Structural Determination of a Trigonal Laccase from Coriolopsis Gallica (CgL) to 1.5 A resolution
ComponentsCORIOLOPSIS GALLICA LACCASE
KeywordsOXIDOREDUCTASE / CATALYTIC DOMAIN / LACCASE / MODELS / MOLECULAR / OXIDATION-REDUCTION / PROTEIN CONFORMATION
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 / Multicopper oxidase, C-terminal / 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 / Multicopper oxidase, C-terminal / 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
ACETATE ION / COPPER (II) ION / Laccase
Similarity search - Component
Biological speciesCORIOLOPSIS GALLICA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRuiz-Arellano, R.R. / Diaz, A. / Ayala, M. / De la Mora, E. / Rudino-Pinera, E.
CitationJournal: To be Published
Title: Metal Site Delocalization Observed in a Model Multicopper Oxidase: An Insight Into Water Release Mechanism
Authors: De la Mora, E. / Morales, N. / Rodriguez-Almazan, G. / Ruiz-Arellano, R.R. / Rudino-Pinira, E.
History
DepositionJul 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
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 / database_PDB_caveat / 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_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.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_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_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Apr 28, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_distant_solvent_atoms / 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 / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn
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 / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 3.1Dec 7, 2022Group: Data collection / Database references / Category: database_2 / pdbx_entity_branch_descriptor
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 4.0Jan 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_distant_solvent_atoms / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn
Item: _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_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
Revision 4.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CORIOLOPSIS GALLICA LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0599
Polymers52,9061
Non-polymers2,1538
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.742, 56.406, 59.173
Angle α, β, γ (deg.)75.67, 73.03, 76.49
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CORIOLOPSIS GALLICA LACCASE


Mass: 52906.469 Da / Num. of mol.: 1 / Fragment: 22-517 / Source method: isolated from a natural source / Source: (natural) CORIOLOPSIS GALLICA (fungus) / Strain: LAC1 / References: UniProt: Q1W6B1

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Sugars , 3 types, 3 molecules

#2: Polysaccharide beta-D-mannopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(4-4)-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
DManpb4-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+4)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(3-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(3-3)-[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: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa3-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Glcp]{[(3+3)][b-D-Allp]{}[(6+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 586 molecules

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


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.48 Å3/Da / Density % sol: 53.29 % / Description: NONE
Crystal growpH: 7
Details: 0.17 M AMMONIUM SULPHATE, 25.5% PEG 8000, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 1.5→43.08 Å / Num. obs: 81678 / % possible obs: 94.4 % / Observed criterion σ(I): 1.97 / Redundancy: 3.9 % / Biso Wilson estimate: 15.04 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.1 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A2G

2a2g


Resolution: 1.5→43.082 Å / SU ML: 0.14 / σ(F): 1.97 / Phase error: 17.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1829 4051 5 %
Rwork0.1634 --
obs0.1643 81678 94.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0973 Å20.8035 Å20.8644 Å2
2---0.0242 Å21 Å2
3---0.1215 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 131 581 4447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0294198
X-RAY DIFFRACTIONf_angle_d2.0255809
X-RAY DIFFRACTIONf_dihedral_angle_d12.5971429
X-RAY DIFFRACTIONf_chiral_restr0.158672
X-RAY DIFFRACTIONf_plane_restr0.013775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51770.23321290.22652666X-RAY DIFFRACTION91
1.5177-1.53620.2541380.22052557X-RAY DIFFRACTION92
1.5362-1.55560.20791470.22172620X-RAY DIFFRACTION92
1.5556-1.57610.23521460.20382644X-RAY DIFFRACTION93
1.5761-1.59770.21731470.20662575X-RAY DIFFRACTION92
1.5977-1.62050.2191330.20012621X-RAY DIFFRACTION93
1.6205-1.64470.21751430.20412630X-RAY DIFFRACTION92
1.6447-1.67040.23071360.19442624X-RAY DIFFRACTION94
1.6704-1.69780.22941440.19312675X-RAY DIFFRACTION93
1.6978-1.72710.20121280.19192662X-RAY DIFFRACTION94
1.7271-1.75850.19681610.18392679X-RAY DIFFRACTION94
1.7585-1.79230.17691260.18562600X-RAY DIFFRACTION93
1.7923-1.82890.22781500.18542700X-RAY DIFFRACTION95
1.8289-1.86860.20151540.18822642X-RAY DIFFRACTION94
1.8686-1.91210.17431550.18092650X-RAY DIFFRACTION93
1.9121-1.95990.21961220.18322652X-RAY DIFFRACTION94
1.9599-2.01290.18841160.1732714X-RAY DIFFRACTION95
2.0129-2.07210.18941420.17732720X-RAY DIFFRACTION95
2.0721-2.1390.1921230.1822689X-RAY DIFFRACTION95
2.139-2.21550.18721440.17052742X-RAY DIFFRACTION96
2.2155-2.30420.17741400.17022696X-RAY DIFFRACTION96
2.3042-2.4090.1941470.16462759X-RAY DIFFRACTION96
2.409-2.5360.19491640.172739X-RAY DIFFRACTION97
2.536-2.69490.19851240.16792740X-RAY DIFFRACTION96
2.6949-2.90290.17831430.16452720X-RAY DIFFRACTION97
2.9029-3.1950.15471440.14912757X-RAY DIFFRACTION97
3.195-3.65710.14731410.14182757X-RAY DIFFRACTION97
3.6571-4.60670.14771360.11892763X-RAY DIFFRACTION97
4.6067-43.09970.17351280.13732634X-RAY DIFFRACTION93

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