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- PDB-8u8q: V290N/S292F Streptomyces coelicolor Laccase -

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Basic information

Entry
Database: PDB / ID: 8u8q
TitleV290N/S292F Streptomyces coelicolor Laccase
ComponentsCopper oxidase
KeywordsOXIDOREDUCTASE / Laccase / Copper
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, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
BORIC ACID / COPPER (II) ION / GLYCINE / HYDROXIDE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Copper oxidase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, J.-X. / Lu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Increasing Reduction Potentials of Type 1 Copper Center and Catalytic Efficiency of Small Laccase from Streptomyces coelicolor through Secondary Coordination Sphere Mutations.
Authors: Wang, J.X. / Vilbert, A.C. / Cui, C. / Mirts, E.N. / Williams, L.H. / Kim, W. / Jessie Zhang, Y. / Lu, Y.
History
DepositionSep 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper oxidase
B: Copper oxidase
C: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,17046
Polymers114,2353
Non-polymers3,93643
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17760 Å2
ΔGint-114 kcal/mol
Surface area28020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.335, 178.335, 179.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Copper oxidase / Laccase


Mass: 38078.215 Da / Num. of mol.: 3 / Mutation: V290N, S292F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO6712 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XAL8

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Non-polymers , 8 types, 222 molecules

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


Mass: 63.546 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#8: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: Crystals were prepared using hanging drop vapor-diffusion technique at room temperature (~296 K). Protein is at a concentration of 18.5 mg/ml in 50 mM H3BO3, 0.1 M NaCl, pH 9.0 buffer. The ...Details: Crystals were prepared using hanging drop vapor-diffusion technique at room temperature (~296 K). Protein is at a concentration of 18.5 mg/ml in 50 mM H3BO3, 0.1 M NaCl, pH 9.0 buffer. The well buffer contains 0.1 M glycine, 0.3-0.6 M NaCl, pH 9.0, and 37-39% (v/v) PEG (polyethylene glycol) monomethyl ether 550. 500 uL of well buffer is added to each well and protein is mixed with well buffer at a 1.5 uL:1.5 uL ratio. The crystal growth time was ca. 1-2 weeks

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→59.57 Å / Num. obs: 79555 / % possible obs: 99.95 % / Redundancy: 14.7 % / Biso Wilson estimate: 57.09 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2429 / Net I/σ(I): 10.71
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 1.874 / Num. unique obs: 7827 / CC1/2: 0.689

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
xia2data scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→56.42 Å / SU ML: 0.3173 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2055 7505 4.95 %
Rwork0.1726 144068 -
obs0.1742 79537 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.32 Å2
Refinement stepCycle: LAST / Resolution: 2.7→56.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 223 179 6870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756837
X-RAY DIFFRACTIONf_angle_d0.94429201
X-RAY DIFFRACTIONf_chiral_restr0.0574927
X-RAY DIFFRACTIONf_plane_restr0.00771212
X-RAY DIFFRACTIONf_dihedral_angle_d11.2494993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.3032240.29454787X-RAY DIFFRACTION100
2.73-2.760.35822960.28354819X-RAY DIFFRACTION100
2.76-2.80.29972250.28744795X-RAY DIFFRACTION100
2.8-2.830.36242370.26024876X-RAY DIFFRACTION100
2.83-2.870.28812800.25594768X-RAY DIFFRACTION100
2.87-2.910.26042150.23754816X-RAY DIFFRACTION100
2.91-2.950.25432870.22844717X-RAY DIFFRACTION99.98
2.95-2.990.26162000.22194871X-RAY DIFFRACTION99.98
2.99-3.040.25342840.20554800X-RAY DIFFRACTION100
3.04-3.090.23132780.19544777X-RAY DIFFRACTION100
3.09-3.140.252170.1964835X-RAY DIFFRACTION100
3.14-3.20.2592190.19624822X-RAY DIFFRACTION100
3.2-3.260.20882450.19474809X-RAY DIFFRACTION100
3.26-3.330.24761930.1864857X-RAY DIFFRACTION99.96
3.33-3.40.17722210.17184816X-RAY DIFFRACTION99.92
3.4-3.480.21812610.18474805X-RAY DIFFRACTION99.94
3.48-3.570.18842700.16734807X-RAY DIFFRACTION100
3.57-3.660.18382420.15944800X-RAY DIFFRACTION99.94
3.66-3.770.22072530.16654800X-RAY DIFFRACTION100
3.77-3.890.16242800.15684758X-RAY DIFFRACTION100
3.89-4.030.20232790.15544755X-RAY DIFFRACTION100
4.03-4.190.19172580.14594808X-RAY DIFFRACTION100
4.19-4.390.18982830.14174771X-RAY DIFFRACTION100
4.39-4.620.16032610.13124795X-RAY DIFFRACTION100
4.62-4.910.14742320.13594811X-RAY DIFFRACTION100
4.91-5.280.18842840.14074773X-RAY DIFFRACTION100
5.28-5.810.18332500.14784809X-RAY DIFFRACTION100
5.82-6.650.19252290.17434839X-RAY DIFFRACTION100
6.66-8.380.23542110.18374842X-RAY DIFFRACTION100
8.38-56.420.18142910.17424730X-RAY DIFFRACTION99.31

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