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- PDB-2h5u: Crystal structure of laccase from Cerrena maxima at 1.9A resolution -

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Basic information

Entry
Database: PDB / ID: 2h5u
TitleCrystal structure of laccase from Cerrena maxima at 1.9A resolution
Componentslaccase
KeywordsOXIDOREDUCTASE / blue multi-copper enzyme / laccase from Cerrena maxima / purification / crystals / X-ray analyses
Function / homology
Function and homology information


lignin catabolic process / hydroquinone:oxygen oxidoreductase activity / laccase / oxidoreductase activity / copper ion binding / extracellular region
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, type 1 / 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 / 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 / Laccase
Similarity search - Component
Biological speciesTrametes maxima (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLyashenko, A.V. / Gabdoulkhakov, A.G. / Zaitsev, V.N. / Lamzin, V.S. / Lindley, P.F. / Bento, I. / Betzel, C. / Zhukhlistova, N.E. / Zhukova, Y.N. / Mikhailov, A.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima
Authors: Lyashenko, A.V. / Zhukhlistova, N.E. / Gabdoulkhakov, A.G. / Zaitsev, V.N. / Bento, I. / Lamzin, V.S. / Betzel, C. / Lindley, P.F. / Koroleva, O.V. / Zhukova, Y.N. / Stepanova, E.V. / ...Authors: Lyashenko, A.V. / Zhukhlistova, N.E. / Gabdoulkhakov, A.G. / Zaitsev, V.N. / Bento, I. / Lamzin, V.S. / Betzel, C. / Lindley, P.F. / Koroleva, O.V. / Zhukova, Y.N. / Stepanova, E.V. / Morgunova, E.Y. / Voelter, W. / Schirwitz, K. / Tishkov, V.I. / Kachalova, G.S. / Cherkashyn, E.A. / Mikhailov, A.M.
History
DepositionMay 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 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 / 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 / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _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_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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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
Remark 999SEQUENCE The sequence of the protein was not available at any sequence database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6699
Polymers53,4751
Non-polymers2,1948
Water9,512528
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.581, 77.101, 130.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer, which presented in the asymmetric unit.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein laccase


Mass: 53475.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trametes maxima (fungus) / Strain: 0275 (Mont)Kraisel of the Polyporaceae family / References: UniProt: D0VWU3*PLUS, laccase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: 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.: 1
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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 2 types, 532 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM sodium citrate, 15% PEG 6000, 0.04M tris-malein-NaOH buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8068 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8068 Å / Relative weight: 1
ReflectionResolution: 1.9→19.27 Å / Num. obs: 39919
Reflection shellResolution: 1.9→1.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.27 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 3.517 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23835 2102 5 %RANDOM
Rwork0.18953 ---
all0.19193 ---
obs0.19193 39919 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.234 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 132 528 4444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214068
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.9695593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09524.863183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87515508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1441514
X-RAY DIFFRACTIONr_chiral_restr0.0640.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023182
X-RAY DIFFRACTIONr_nbd_refined0.1750.21946
X-RAY DIFFRACTIONr_nbtor_refined0.310.22732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2569
X-RAY DIFFRACTIONr_metal_ion_refined0.1550.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.244
X-RAY DIFFRACTIONr_mcbond_it0.2821.52562
X-RAY DIFFRACTIONr_mcangle_it0.50324069
X-RAY DIFFRACTIONr_scbond_it0.73631691
X-RAY DIFFRACTIONr_scangle_it1.0944.51521
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 145 -
Rwork0.245 2755 -
obs--100 %

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