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- PDB-2hzh: Crystal structure of laccase from Coriolus zonatus at 2.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 2hzh
TitleCrystal structure of laccase from Coriolus zonatus at 2.6 A resolution
Componentslaccase
KeywordsOXIDOREDUCTASE / blue multi-copper enzyme / laccase from Coriolus zonatus / purification / crystals / X-ray analyses
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 / alpha-D-mannopyranose / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Laccase 2
Similarity search - Component
Biological speciesTrametes ochracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLyashenko, A.V. / Mikhailov, A.M.
CitationJournal: To be published
Title: Crystal structure of laccase from Coriolus zonatus at 2.6 A resolution
Authors: Lyashenko, A.V. / Zhukhlistova, N.E. / Gabdoulkhakov, A.G. / Zhukova, Y.N. / Voelter, W. / Zaitsev, V.N. / Bento, I. / Stepanova, E.V. / Kachalova, G.S. / Koroleva, O.V. / Betzel, C. / ...Authors: Lyashenko, A.V. / Zhukhlistova, N.E. / Gabdoulkhakov, A.G. / Zhukova, Y.N. / Voelter, W. / Zaitsev, V.N. / Bento, I. / Stepanova, E.V. / Kachalova, G.S. / Koroleva, O.V. / Betzel, C. / Lindley, P.F. / Mikhailov, A.M. / Tishkov, V.I. / Morgunova, E.Y.
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 17, 2016Group: Derived calculations
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
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 / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE A UNP REFERENCE SEQUENCE FOR THE PROTEIN WAS NOT AVAILABLE 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)54,12210
Polymers52,8031
Non-polymers1,3199
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.930, 168.930, 69.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsThe biological assembly is a monomer in the asymmetric unit

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Components

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Protein , 1 types, 1 molecules A

#1: Protein laccase /


Mass: 52802.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trametes ochracea (fungus) / References: UniProt: Q8TG94*PLUS

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Sugars , 3 types, 5 molecules

#2: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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, 120 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 5.36 Å3/Da / Density % sol: 76.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: The crystallizing solution (volume 6 ml) contained the protein at a concentration of 8 mg/ml in 50 mM sodium citrate, 0.1 M ammonium sulfate, and 12.5% (w/v) PEG 4000 in 0.05M sodium acetate ...Details: The crystallizing solution (volume 6 ml) contained the protein at a concentration of 8 mg/ml in 50 mM sodium citrate, 0.1 M ammonium sulfate, and 12.5% (w/v) PEG 4000 in 0.05M sodium acetate buffer at pH 4.6., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 6, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.6→145.86 Å / Num. obs: 35011 / % possible obs: 0.9507 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.02 %
Reflection shellResolution: 2.6→2.62 Å / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→145.86 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.652 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23792 1691 5 %RANDOM
Rwork0.21135 ---
all0.21272 ---
obs0.21272 31805 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.6→145.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 73 116 3924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223914
X-RAY DIFFRACTIONr_angle_refined_deg1.171.9385382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2325498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33724.914175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69115496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7991512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023084
X-RAY DIFFRACTIONr_nbd_refined0.2060.21769
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2186
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.23
X-RAY DIFFRACTIONr_mcbond_it0.3781.52545
X-RAY DIFFRACTIONr_mcangle_it0.68424024
X-RAY DIFFRACTIONr_scbond_it0.73931547
X-RAY DIFFRACTIONr_scangle_it1.1624.51358
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 116 -
Rwork0.309 2289 -
obs--93.33 %

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