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- PDB-3fu7: Melanocarpus albomyces laccase crystal soaked (4 sec) with 2,6-di... -

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Basic information

Entry
Database: PDB / ID: 3fu7
TitleMelanocarpus albomyces laccase crystal soaked (4 sec) with 2,6-dimethoxyphenol
Components(Laccase-1) x 2
KeywordsOXIDOREDUCTASE / Laccase / multicopper oxidase / complex structure / 2 / 6-dimethoxyphenol / oxidation of phenolic compounds / Glycoprotein / Lignin degradation / Metal-binding
Function / homology
Function and homology information


extraorganismal space / lignin catabolic process / hydroquinone:oxygen oxidoreductase activity / laccase / cellulose catabolic process / copper ion binding
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal ...Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2,6-dimethoxyphenol / COPPER (II) ION / 4-(2,6-dimethoxyphenoxy)-2,6-dimethoxyphenol / 2,6-dimethoxycyclohexa-2,5-diene-1,4-dione / OXYGEN MOLECULE / Laccase-1
Similarity search - Component
Biological speciesMelanocarpus albomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsKallio, J.P. / Hakulinen, N. / Rouvinen, J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure Function Studies of a Melanocarpus albomyces Laccase Suggest a Pathway for Oxidation of Phenolic Compounds.
Authors: Kallio, J.P. / Auer, S. / Janis, J. / Andberg, M. / Kruus, K. / Rouvinen, J. / Koivula, A. / Hakulinen, N.
History
DepositionJan 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / 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_validate_chiral / pdbx_validate_close_contact / 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_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 / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Sep 6, 2023Group: 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
Revision 2.2Nov 22, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Laccase-1
B: Laccase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,16234
Polymers123,7042
Non-polymers7,45932
Water17,168953
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-40 kcal/mol
Surface area38910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.120, 62.100, 124.630
Angle α, β, γ (deg.)90.00, 96.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Laccase-1 / Benzenediol:oxygen oxidoreductase 1 / Urishiol oxidase 1 / Diphenol oxidase 1 / Ligninolytic phenoloxidase


Mass: 61858.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melanocarpus albomyces (fungus) / Strain: VTT D-96490 / Gene: LAC1 / Production host: Trichoderma reesei (fungus) / Strain (production host): RUTC-30 / References: UniProt: Q70KY3, laccase
#2: Protein Laccase-1 / Benzenediol:oxygen oxidoreductase 1 / Urishiol oxidase 1 / Diphenol oxidase 1 / Ligninolytic phenoloxidase


Mass: 61845.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melanocarpus albomyces (fungus) / Strain: VTT D-96490 / Gene: LAC1 / Production host: Trichoderma reesei (fungus) / Strain (production host): RUTC-30 / References: UniProt: Q70KY3, laccase

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Sugars , 4 types, 14 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 5
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
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 971 molecules

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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-3DM / 2,6-dimethoxyphenol


Mass: 154.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10O3
#12: Chemical ChemComp-D2M / 4-(2,6-dimethoxyphenoxy)-2,6-dimethoxyphenol


Mass: 306.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18O6
#13: Chemical ChemComp-KIA / 2,6-dimethoxycyclohexa-2,5-diene-1,4-dione / 2,6-dimethoxy-p-benzoquinone


Mass: 168.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O4
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 953 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15 % PMME 2000, 0,2 M ammonium sulphate, 0,1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.365 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2006 / Details: mirrors
RadiationMonochromator: Double crystal Si[111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.365 Å / Relative weight: 1
ReflectionResolution: 1.67→20 Å / Num. all: 149347 / Num. obs: 149347 / % possible obs: 97.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.068 / Net I/σ(I): 11.5
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 6162 / Rsym value: 0.25 / % possible all: 77.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q9o

2q9o


Resolution: 1.67→19.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.883 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22033 7468 5 %RANDOM
Rwork0.18881 ---
all0.19038 149347 --
obs0.19038 141878 100 %-
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: 17.022 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20.22 Å2
2---0.45 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.67→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8739 0 462 953 10154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0219731
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.98213428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22951166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1124.236458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.349151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.451556
X-RAY DIFFRACTIONr_chiral_restr0.0940.21500
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027616
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.24536
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.26675
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2882
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.731.55823
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16329390
X-RAY DIFFRACTIONr_scbond_it1.88434400
X-RAY DIFFRACTIONr_scangle_it2.854.54038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.715 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 487 -
Rwork0.207 9249 -
obs--100 %

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