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- PDB-8u8p: S292F Streptomyces coelicolor Laccase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8u8p
TitleS292F 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 / Multicopper oxidase, C-terminal / 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: 2.2 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)118,12546
Polymers114,1903
Non-polymers3,93643
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17280 Å2
ΔGint-107 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.221, 177.221, 177.399
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: 38063.242 Da / Num. of mol.: 3 / Mutation: 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, 473 molecules

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


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-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GLY / GLYCINE / Glycine


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


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


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


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


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / 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 / pH: 9
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: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.2→62.69 Å / Num. obs: 142572 / % possible obs: 99.97 % / Redundancy: 13.4 % / Biso Wilson estimate: 38.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1663 / Net I/σ(I): 11.31
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 1.525 / Num. unique obs: 14126 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
BOSdata collection
xia2data scaling
PHENIX1.20.1-4487phasing
PHENIX1.20.1_4487refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→62.69 Å / SU ML: 0.202 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.7106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 7057 4.95 %
Rwork0.1648 135489 -
obs0.1656 142546 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→62.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6457 0 223 430 7110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726826
X-RAY DIFFRACTIONf_angle_d0.82779187
X-RAY DIFFRACTIONf_chiral_restr0.0587928
X-RAY DIFFRACTIONf_plane_restr0.00651208
X-RAY DIFFRACTIONf_dihedral_angle_d11.4555992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.28782090.24884492X-RAY DIFFRACTION100
2.23-2.250.27742050.23084485X-RAY DIFFRACTION100
2.25-2.280.23762180.22284516X-RAY DIFFRACTION100
2.28-2.310.2392360.21054430X-RAY DIFFRACTION100
2.31-2.340.20762100.21064450X-RAY DIFFRACTION100
2.34-2.370.23112410.20264489X-RAY DIFFRACTION100
2.37-2.40.21692440.20034467X-RAY DIFFRACTION99.98
2.4-2.440.24012280.19894467X-RAY DIFFRACTION100
2.44-2.480.1942220.20144499X-RAY DIFFRACTION100
2.48-2.520.23481920.19254464X-RAY DIFFRACTION100
2.52-2.560.21982350.17974502X-RAY DIFFRACTION100
2.56-2.610.21352380.17114502X-RAY DIFFRACTION100
2.61-2.660.2162110.17844484X-RAY DIFFRACTION100
2.66-2.710.20581800.16894518X-RAY DIFFRACTION100
2.71-2.770.18392540.15974491X-RAY DIFFRACTION100
2.77-2.840.15762290.15644476X-RAY DIFFRACTION99.98
2.84-2.910.19052480.15474490X-RAY DIFFRACTION100
2.91-2.990.18132200.15434538X-RAY DIFFRACTION100
2.99-3.070.15262380.13924485X-RAY DIFFRACTION100
3.07-3.170.16712200.13694558X-RAY DIFFRACTION100
3.17-3.290.11752810.13384423X-RAY DIFFRACTION100
3.29-3.420.1452300.14364559X-RAY DIFFRACTION99.98
3.42-3.570.17652850.14234444X-RAY DIFFRACTION99.96
3.57-3.760.16582260.15134537X-RAY DIFFRACTION100
3.76-40.18532570.16234535X-RAY DIFFRACTION100
4-4.310.15462950.15294502X-RAY DIFFRACTION100
4.31-4.740.15392590.14634563X-RAY DIFFRACTION100
4.74-5.420.17792460.15124607X-RAY DIFFRACTION100
5.42-6.830.19572320.17834696X-RAY DIFFRACTION99.98
6.83-62.690.22962680.20044820X-RAY DIFFRACTION99.55

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