[English] 日本語
Yorodumi
- PDB-1hfu: TYPE-2 CU-DEPLETED LACCASE FROM COPRINUS CINEREUS at 1.68 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hfu
TitleTYPE-2 CU-DEPLETED LACCASE FROM COPRINUS CINEREUS at 1.68 A resolution
ComponentsLACCASE 1
KeywordsOXIDOREDUCTASE / LACCASE / BLUE MULTI-COPPER OXIDASE / TYPE-2 COPPER DEPLETED / GLYCOPROTEIN
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding / extracellular region
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / 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, copper-binding site / Multicopper oxidases signature 2. / 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
2alpha-alpha-mannobiose / COPPER (II) ION / laccase
Similarity search - Component
Biological speciesCOPRINUS CINEREUS (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsDucros, V. / Brzozowski, A.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of the Laccase from Coprinus Cinereus at 1.68A Resolution: Evidence for Different Type 2 Cu-Depleted Isoforms
Authors: Ducros, V. / Brzozowski, A.M. / Wilson, K.S. / Ostergaard, P. / Schneider, P. / Svendson, A. / Davies, G.J.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of the Type-2 Cu Depleted Laccase from Coprinus Cinereus at 2.2 A Resolution
Authors: Ducros, V. / Brzozowski, A.M. / Wilson, K.S. / Brown, S.H. / Ostergaard, P. / Schneider, P. / Yaver, D.S. / Pedersen, A.H. / Davies, G.J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary X-Ray Analysis of the Laccase from Coprinus Cinereus.
Authors: Ducros, V. / Davies, G.J. / Lawson, D.M. / Wilson, K.S. / Brown, S.H. / Ostergaard, P. / Pedersen, A.H. / Schneider, P. / Yaver, D.S. / Brzozowski, A.M.
History
DepositionDec 8, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2001Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Sep 17, 2014Group: Non-polymer description
Revision 2.0Sep 11, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / exptl_crystal_grow / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / 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_atom_id / _atom_site.auth_comp_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 / _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _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_alt_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_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_alt_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_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 3.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LACCASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3676
Polymers54,4091
Non-polymers9575
Water8,305461
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.120, 84.560, 139.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL_UNIT: MONOMER

-
Components

#1: Protein LACCASE 1 /


Mass: 54409.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COPRINUS CINEREUS (fungus) / Production host: ASPERGILLUS ORYZAE (mold) / Strain (production host): A. ORYZAE A1560 / References: UniProt: Q9Y780, laccase
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-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.: 1
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)][a-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: PROTEIN WAS AT 30MG/ML IN 100MM ACETATE BUFFER PH 5.5. CRYSTALS GROW FROM 20-30% PEG 8000
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Details: Ducros, V., (1997) Acta Crystallogr.,Sect.D, D53, 605.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
210 mMacetate1drop
326-30 %(v/v)PEG80001reservoir
40.1 Macetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: LONG FOCUSSING MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→15 Å / Num. obs: 61668 / % possible obs: 96 % / Redundancy: 4.6 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 22.2
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 10 / Rsym value: 0.275 / % possible all: 91.9
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 96 %
Reflection shell
*PLUS
% possible obs: 92 %

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A65

1a65


Resolution: 1.68→15 Å / SU B: 2.197 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.1007
Details: THE OCCUPANCY OF SOME ATOMS OF RESIDUES: GLN164, MET459, VAL503 ARE SET TO ZERO DUE TO DISORDER; THEY WERE MODELLED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 2935 5 %RANDOM
Rwork0.184 ---
obs-58721 96 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.68→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 53 461 4341
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8133
X-RAY DIFFRACTIONp_mcangle_it2.3695
X-RAY DIFFRACTIONp_scbond_it2.7164
X-RAY DIFFRACTIONp_scangle_it3.546
X-RAY DIFFRACTIONp_plane_restr0.025
X-RAY DIFFRACTIONp_chiral_restr0.1310.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2380.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.27
X-RAY DIFFRACTIONp_staggered_tor13.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.181 / Rfactor Rfree: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19 Å2

+
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://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