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- PDB-3cg8: Laccase from Streptomyces coelicolor -

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Basic information

Entry
Database: PDB / ID: 3cg8
TitleLaccase from Streptomyces coelicolor
Componentslaccase
KeywordsOXIDOREDUCTASE / two-domain laccase / multicopper blue protein
Function / homology
Function and homology information


oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / OXYGEN ATOM / Copper oxidase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.679 Å
AuthorsSkalova, T. / Dohnalek, J. / Ostergaard, L.H. / Ostergaard, P.R. / Kolenko, P. / Duskova, J. / Hasek, J.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: The Structure of the Small Laccase from Streptomyces coelicolor Reveals a Link between Laccases and Nitrite Reductases.
Authors: Skalova, T. / Dohnalek, J. / Ostergaard, L.H. / Ostergaard, P.R. / Kolenko, P. / Duskova, J. / Stepankova, A. / Hasek, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and preliminary X-ray diffraction analysis of the small laccase from Streptomyces coelicolor
Authors: Skalova, T. / Dohnalek, J. / Ostergaard, L.H. / Ostergaard, P.R. / Kolenko, P. / Duskova, J. / Hasek, J.
History
DepositionMar 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,57823
Polymers110,7963
Non-polymers1,78220
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint-137 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.868, 180.868, 177.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein laccase / E.C.1.10.3.2


Mass: 36932.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Description: TAKA amylase promoter / Gene: SC4C6.22 / Plasmid: pLAQ029 / Production host: Aspergillus oryzae (mold) / Strain (production host): ToC1512 / References: UniProt: Q9XAL8, laccase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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

Crystal
ID
1
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop939 % (v/v) PEG monomethyl ether 550, 0.1 M NaCl, 0.1 M glycine, pH 9.0; 2:1 protein:reservoir ratio in a drop; data from this crystal were used for structure refinement, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop745 % (w/v) Jeffamine ED-2001, pH 7.0, 0.05 M HEPES, pH 7.0; data from this crystal were consulted during structure refinement but not used as refinement target, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.3775, 1.380, 0.954
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2007 / Details: Si(111) monochromator and mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.37751
21.381
30.9541
ReflectionRedundancy: 29 % / Av σ(I) over netI: 6.1 / Number: 2348328 / Rmerge(I) obs: 0.113 / Χ2: 0.77 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 80881 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815010010.0561.36728.4
4.625.8110010.0771.35529.5
4.034.6210010.0680.88129.9
3.664.0310010.0880.72829.9
3.43.6610010.1110.65529.9
3.23.410010.1480.55129.9
3.043.210010.210.52529.9
2.913.0410010.3040.52729.9
2.82.9110010.440.53629
2.72.899.910.5960.54224.1
ReflectionResolution: 2.65→50 Å / Num. all: 80263 / Num. obs: 80263 / % possible obs: 94.1 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -999 / Redundancy: 17 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Χ2: 1.116 / Net I/σ(I): 11.6
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 9.4 / Num. unique all: 5942 / Rsym value: 0.64 / Χ2: 1.194 / % possible all: 70.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MxCuBEdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.679→28.54 Å / Cor.coef. Fo:Fc: 0.949 / SU B: 3.634 / SU ML: 0.077 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / Stereochemistry target values: REFMAC5 DICTIONARY / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1569 -RANDOM
Rwork0.172 ---
all0.172 78462 --
obs0.172 78462 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.679→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6321 0 71 360 6752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216557
X-RAY DIFFRACTIONr_bond_other_d0.0010.024433
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9278872
X-RAY DIFFRACTIONr_angle_other_deg0.886310713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25523.025314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36815993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6151545
X-RAY DIFFRACTIONr_chiral_restr0.0920.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021388
X-RAY DIFFRACTIONr_nbd_refined0.1910.21169
X-RAY DIFFRACTIONr_nbd_other0.2090.24554
X-RAY DIFFRACTIONr_nbtor_refined0.1860.23142
X-RAY DIFFRACTIONr_nbtor_other0.0920.23514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2353
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1120.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.210
X-RAY DIFFRACTIONr_mcbond_it1.1721.55053
X-RAY DIFFRACTIONr_mcbond_other0.1461.51698
X-RAY DIFFRACTIONr_mcangle_it1.32126420
X-RAY DIFFRACTIONr_scbond_it2.06732968
X-RAY DIFFRACTIONr_scangle_it2.934.52452
LS refinement shellResolution: 2.679→2.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.367 5977 -
obs--99.58 %

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