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- PDB-1gyc: CRYSTAL STRUCTURE DETERMINATION AT ROOM TEMPERATURE OF A LACCASE ... -

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Basic information

Entry
Database: PDB / ID: 1gyc
TitleCRYSTAL STRUCTURE DETERMINATION AT ROOM TEMPERATURE OF A LACCASE FROM TRAMETES VERSICOLOR IN ITS OXIDISED FORM CONTAINING A FULL COMPLEMENT OF COPPER IONS
ComponentsLACCASE 2
KeywordsOXIDOREDUCTASE / LACCASE / DIPHENOL OXIDASE / LIGNIN DEGRADATION
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, 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 / ISOPROPYL ALCOHOL / Laccase-2
Similarity search - Component
Biological speciesTRAMETES VERSICOLOR (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChoinowski, T. / Antorini, M. / Piontek, K.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of a Laccase from the Fungus Trametes Versicolor at 1.90-A Resolution Containing a Full Complement of Coppers.
Authors: Piontek, K. / Antorini, M. / Choinowski, T.
#1: Journal: Biochim.Biophys.Acta / Year: 2002
Title: Purificcation, Crystallisation and X-Ray Diffraction Study of Fully Functional Laccases from Two Ligninolytic Fungi
Authors: Antorini, M. / Herpoel-Gimbertchoinowski, I. / Sigoillot-C, J. / Asther, M. / Winterhalter, K.
History
DepositionApr 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LACCASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,98913
Polymers53,6781
Non-polymers2,31112
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.681, 84.977, 91.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LACCASE 2 / / BENZENEDIOL\:OXYGEN OXIDOREDUCTASE / URISHIOL OXIDASE / DIPHENOL OXIDASE / LACCASE I


Mass: 53677.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRAMETES VERSICOLOR (fungus) / References: UniProt: Q12718, laccase

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Sugars , 2 types, 6 molecules

#2: 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.: 3
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
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 3 types, 596 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSWISS-PROT ENTRY Q12178 HAS THE CLOSEST AGREEMENT WITH THE SEQUENCE OF THE CRYSTALLIZED STRUCTURE. ...SWISS-PROT ENTRY Q12178 HAS THE CLOSEST AGREEMENT WITH THE SEQUENCE OF THE CRYSTALLIZED STRUCTURE. HOWEVER, THE SEQUENCE OF THE STRUCTURE DIFFERS FROM THE SWISS-PROT ENTRY IS SEVERAL PLACES, AND THESE VARIATIONS ARE NOT LISTED IN ENTRY Q12178: V5A, V31F, V259I, T343S, D460E

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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: 2.61 Å3/Da / Density % sol: 52.53 %
Crystal growpH: 5.6
Details: 20% (W/V) PEG8000, 20% (V/V) ISOPROPANOL, 100 MM SODIUM CITRATE PH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Antorini, M., (2002) Biochim.Biophys.Acta, 1594, 109.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG80001reservoir
220 %isopropanol1reservoir
3100 mMsodium citrate1reservoirpH5.6
425 mMsodium acetate1droppH5.
510 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.847
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.847 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 52154 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 99.7 %
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Rmerge(I) obs: 0.38

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Processing

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

1a65


Resolution: 1.9→17.9 Å / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2632 5 %RANDOM
Rwork0.159 ---
obs-51746 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→17.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 138 590 4530
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.026
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2.02 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.205 / Total num. of bins used: 15

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