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- PDB-8u8s: Y229F/S292F Streptomyces coelicolor Laccase -

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Basic information

Entry
Database: PDB / ID: 8u8s
TitleY229F/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: 2.63 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)118,07746
Polymers114,1423
Non-polymers3,93643
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17540 Å2
ΔGint-114 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.351, 176.351, 176.210
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: 38047.242 Da / Num. of mol.: 3 / Mutation: Y229F, 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, 278 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.: 235 / 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: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.63→78.87 Å / Num. obs: 82693 / % possible obs: 99.98 % / Redundancy: 13.3 % / Biso Wilson estimate: 46.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1839 / Net I/σ(I): 12.37
Reflection shellResolution: 2.63→2.724 Å / Rmerge(I) obs: 1.204 / Num. unique obs: 8103 / CC1/2: 0.744

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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: 2.63→78.87 Å / SU ML: 0.2824 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.5344
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1988 7979 5.06 %
Rwork0.1679 149694 -
obs0.1694 82685 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.2 Å2
Refinement stepCycle: LAST / Resolution: 2.63→78.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6454 0 223 235 6912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00696823
X-RAY DIFFRACTIONf_angle_d0.9039181
X-RAY DIFFRACTIONf_chiral_restr0.0553928
X-RAY DIFFRACTIONf_plane_restr0.00771208
X-RAY DIFFRACTIONf_dihedral_angle_d12.1729989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.660.40122550.30854951X-RAY DIFFRACTION100
2.66-2.690.29382580.28444949X-RAY DIFFRACTION100
2.69-2.720.29152650.26815010X-RAY DIFFRACTION100
2.72-2.760.27132720.25515026X-RAY DIFFRACTION100
2.76-2.790.23473560.22954895X-RAY DIFFRACTION100
2.79-2.830.2932560.22285027X-RAY DIFFRACTION100
2.83-2.870.27732580.20634957X-RAY DIFFRACTION100
2.87-2.920.22852420.20785012X-RAY DIFFRACTION100
2.92-2.960.23512870.20254995X-RAY DIFFRACTION100
2.96-3.010.28822420.19584978X-RAY DIFFRACTION100
3.01-3.060.23183080.18444983X-RAY DIFFRACTION100
3.06-3.120.18262180.18215005X-RAY DIFFRACTION100
3.12-3.180.23352670.18415014X-RAY DIFFRACTION100
3.18-3.240.18142780.18465023X-RAY DIFFRACTION100
3.24-3.310.21892440.16655007X-RAY DIFFRACTION100
3.31-3.390.22242220.16245020X-RAY DIFFRACTION99.94
3.39-3.480.18012790.16044944X-RAY DIFFRACTION100
3.48-3.570.17173210.15134993X-RAY DIFFRACTION99.96
3.57-3.670.21713250.17144916X-RAY DIFFRACTION99.98
3.67-3.790.21762180.16325046X-RAY DIFFRACTION100
3.79-3.930.16512920.17334936X-RAY DIFFRACTION100
3.93-4.090.1812280.14895030X-RAY DIFFRACTION100
4.09-4.270.18852260.13185026X-RAY DIFFRACTION100
4.27-4.50.13551910.12695118X-RAY DIFFRACTION100
4.5-4.780.18182730.13314966X-RAY DIFFRACTION100
4.78-5.150.15142820.13084941X-RAY DIFFRACTION100
5.15-5.670.13552590.13845034X-RAY DIFFRACTION100
5.67-6.480.19932770.15654959X-RAY DIFFRACTION100
6.49-8.170.21123030.17594958X-RAY DIFFRACTION100
8.17-78.870.16882770.17474975X-RAY DIFFRACTION99.68

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