[English] 日本語
Yorodumi
- PDB-1kya: ACTIVE LACCASE FROM TRAMETES VERSICOLOR COMPLEXED WITH 2,5-XYLIDINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kya
TitleACTIVE LACCASE FROM TRAMETES VERSICOLOR COMPLEXED WITH 2,5-XYLIDINE
ComponentsLACCASE
KeywordsOXIDOREDUCTASE / BLUE-COPPER
Function / homology
Function and homology information


lignin catabolic process / 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, type 1 / Multicopper oxidase / 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, 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
COPPER (II) ION / TETRAHYDROPYRAN / 2,5-DIMETHYLANILINE / laccase
Similarity search - Component
Biological speciesTrametes versicolor (turkey-tail fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBertrand, T. / Jolivalt, C. / Briozzo, P. / Caminade, E. / Joly, N. / Madzak, C. / Mougin, C.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal structure of a four-copper laccase complexed with an arylamine: insights into substrate recognition and correlation with kinetics.
Authors: Bertrand, T. / Jolivalt, C. / Briozzo, P. / Caminade, E. / Joly, N. / Madzak, C. / Mougin, C.
History
DepositionFeb 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.label_asym_id / _struct_conn.pdbx_dist_value / _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_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 1.4Aug 16, 2023Group: Data collection / Database references ...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 / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LACCASE
B: LACCASE
C: LACCASE
D: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,71760
Polymers213,4684
Non-polymers8,24956
Water14,232790
1
A: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,46315
Polymers53,3671
Non-polymers2,09614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,63517
Polymers53,3671
Non-polymers2,26816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,29113
Polymers53,3671
Non-polymers1,92412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,32815
Polymers53,3671
Non-polymers1,96114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.720, 110.520, 123.201
Angle α, β, γ (deg.)90, 103.436, 90
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 31 molecules ABCD

#1: Protein
LACCASE / LACCASE B


Mass: 53366.875 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Trametes versicolor (turkey-tail fungus) / Strain: ATCC 32745 / References: UniProt: Q96UT7, laccase
#2: 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.: 27
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

-
Non-polymers , 4 types, 819 molecules

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


Mass: 63.546 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-PYE / TETRAHYDROPYRAN


Mass: 86.132 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C5H10O
#5: Chemical
ChemComp-XYD / 2,5-DIMETHYLANILINE / 2,5-XYLIDINE


Mass: 121.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H11N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Zinc Acetate, Sodium cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Bertrand, T., (2002) Acta Crystallogr., Sect.D, 58, 319.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
124 mg/mlprotein1drop
218 %(w/v)PEG80001reservoir
30.2 Mzinc acetate1reservoir
40.1 Msodium cacodylate1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 22, 2001 / Details: Osmic focusing optics
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. all: 89441 / Num. obs: 83644 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 22 % / Rsym value: 0.114 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.49 Å / Rsym value: 0.266 / % possible all: 71.6
Reflection
*PLUS
Lowest resolution: 35 Å

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A65

1a65


Resolution: 2.4→35 Å / Isotropic thermal model: OVERALL ANISOTROPIC B / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: DISORDERED RESIDUES (A 101, A 363, A 442, A 460, A 482, B 101, B 363, B 442, B 460, B 482, C 101, C 363, C 442, C 460, C 482, D 101, D 363, D 442, D 460, D 482) WERE NOT INCLUDED IN MODEL. ...Details: DISORDERED RESIDUES (A 101, A 363, A 442, A 460, A 482, B 101, B 363, B 442, B 460, B 482, C 101, C 363, C 442, C 460, C 482, D 101, D 363, D 442, D 460, D 482) WERE NOT INCLUDED IN MODEL. HIS 55, HIS 91, HIS 402 AND ASP 473 ARE LINKED TO NON-ATTRIBUTED ELECTRONIC DENSITY IN MOLECULES A, B, C AND D: WATER MOLECULES WERE PLACED IN INSTEAD.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 4245 -RANDOM
Rwork0.253 ---
all-89441 --
obs-83612 93.5 %-
Displacement parametersBiso mean: 39.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15012 0 484 790 16286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_bond_d0.0075
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 35 Å / % reflection Rfree: 5 % / Rfactor obs: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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