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- PDB-1kya: ACTIVE LACCASE FROM TRAMETES VERSICOLOR COMPLEXED WITH 2,5-XYLIDINE -

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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


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, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin ...Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / 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
COPPER (II) ION / TETRAHYDROPYRAN / 2,5-DIMETHYLANILINE / Laccase B
Similarity search - Component
Biological speciesTrametes versicolor (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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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 (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

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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

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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: 2.72 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

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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

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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

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