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- PDB-3kw8: Two-domain laccase from Streptomyces coelicolor at 2.3 A resolution -

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Basic information

Entry
Database: PDB / ID: 3kw8
TitleTwo-domain laccase from Streptomyces coelicolor at 2.3 A resolution
ComponentsPutative copper oxidase
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 / : / TRIETHYLENE GLYCOL / Copper oxidase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSkalova, T. / Dohnalek, J. / Kolenko, P. / Duskova, J. / Stepankova, A. / Hasek, J. / Ostergaard, L.H. / Ostergaard, P.R.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of laccase from Streptomyces coelicolor after soaking with potassium hexacyanoferrate and at an improved resolution of 2.3 A
Authors: Skalova, T. / Duskova, J. / Hasek, J. / Stepankova, A. / Koval, T. / Ostergaard, L.H. / Dohnalek, J.
#1: 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.
#2: 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
DepositionDec 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _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_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: Putative copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,57413
Polymers30,3791
Non-polymers1,19512
Water4,216234
1
A: Putative copper oxidase
hetero molecules

A: Putative copper oxidase
hetero molecules

A: Putative copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,72239
Polymers91,1373
Non-polymers3,58536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10720 Å2
ΔGint-47 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.723, 176.723, 176.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-501-

FE

21A-787-

HOH

31A-844-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative copper oxidase / laccase


Mass: 30378.855 Da / Num. of mol.: 1 / Fragment: residues 42-317
Source method: isolated from a genetically manipulated source
Details: TAKA amylase promoter / Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SC4C6.22 / Plasmid: PLAQ029 / Production host: Aspergillus oryzae (mold) / Strain (production host): TOC1512 / References: UniProt: Q9XAL8, laccase

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Non-polymers , 6 types, 246 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsFE IN THIS STRUCTURE IS A PART OF A HEXACYANOFERRATE ION.

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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: 7.569955 Å3/Da / Density % sol: 83.751556 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 40 %(v/v) PEG 550 monomethyl ether, 0.1M NaCl, 0.1M glycine, 50mM potassium hexacyanoferrate , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2007 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 42751 / Num. obs: 42751 / % possible obs: 100 % / Redundancy: 24.1 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 33.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 24.6 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2077 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CG8

3cg8


Resolution: 2.29→38.56 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.041 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17817 1326 3.1 %RANDOM
Rwork0.16143 ---
all0.16193 41054 --
obs0.16193 41054 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.356 Å2
Refinement stepCycle: LAST / Resolution: 2.29→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 63 234 2418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212247
X-RAY DIFFRACTIONr_bond_other_d0.0010.021547
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9363025
X-RAY DIFFRACTIONr_angle_other_deg0.85333743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.695272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05422.963108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81715337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1051516
X-RAY DIFFRACTIONr_chiral_restr0.090.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02470
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7941.51342
X-RAY DIFFRACTIONr_mcbond_other0.1991.5569
X-RAY DIFFRACTIONr_mcangle_it1.5222159
X-RAY DIFFRACTIONr_scbond_it2.3273905
X-RAY DIFFRACTIONr_scangle_it3.7984.5866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.294→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 94 -
Rwork0.224 2966 -
obs--98.68 %

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