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- PDB-8u8r: Y229F/V290N/S292F Streptomyces coelicolor Laccase -

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Basic information

Entry
Database: PDB / ID: 8u8r
TitleY229F/V290N/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: 2.86 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)118,12246
Polymers114,1873
Non-polymers3,93643
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17780 Å2
ΔGint-115 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.355, 177.355, 176.956
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: 38062.215 Da / Num. of mol.: 3 / Mutation: Y229F, 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, 187 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-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
#4: Chemical
ChemComp-GLY / 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


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 144 / 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

CrystalDensity Matthews: 6.27 Å3/Da / Density % sol: 80.38 %
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: 5.0.2 / 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: 2.86→72.38 Å / Num. obs: 65563 / % possible obs: 99.96 % / Redundancy: 13.4 % / Biso Wilson estimate: 56.35 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.2833 / Net I/σ(I): 10.32
Reflection shellResolution: 2.86→2.962 Å / Rmerge(I) obs: 1.889 / Num. unique obs: 6445 / CC1/2: 0.607

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Processing

Software
NameVersionClassification
BOSdata collection
xia2data reduction
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→62.7 Å / SU ML: 0.3422 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1998
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2137 6114 4.91 %
Rwork0.1815 118420 -
obs0.183 65553 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.81 Å2
Refinement stepCycle: LAST / Resolution: 2.86→62.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 223 144 6832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00736834
X-RAY DIFFRACTIONf_angle_d0.93849195
X-RAY DIFFRACTIONf_chiral_restr0.056927
X-RAY DIFFRACTIONf_plane_restr0.00751212
X-RAY DIFFRACTIONf_dihedral_angle_d11.6091990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.890.31962350.28923913X-RAY DIFFRACTION99.98
2.89-2.930.29191770.29073940X-RAY DIFFRACTION100
2.93-2.960.32611740.27394002X-RAY DIFFRACTION99.98
2.96-30.27882170.2543943X-RAY DIFFRACTION100
3-3.040.34861870.25633935X-RAY DIFFRACTION100
3.04-3.080.34722040.2473970X-RAY DIFFRACTION100
3.08-3.120.29382690.23583901X-RAY DIFFRACTION99.98
3.12-3.170.26732380.23323926X-RAY DIFFRACTION100
3.17-3.220.22241820.22063970X-RAY DIFFRACTION100
3.22-3.270.26071460.20693964X-RAY DIFFRACTION99.9
3.27-3.330.20952030.20343959X-RAY DIFFRACTION100
3.33-3.390.21692040.19423945X-RAY DIFFRACTION99.98
3.39-3.460.26282070.18733928X-RAY DIFFRACTION99.95
3.46-3.530.20682820.18023910X-RAY DIFFRACTION99.93
3.53-3.60.19932320.18013873X-RAY DIFFRACTION100
3.6-3.690.27132010.17083994X-RAY DIFFRACTION99.95
3.69-3.780.15671780.16893950X-RAY DIFFRACTION100
3.78-3.880.17121850.16453978X-RAY DIFFRACTION100
3.88-40.19272300.15913923X-RAY DIFFRACTION100
4-4.120.15052200.14973950X-RAY DIFFRACTION100
4.12-4.270.18172040.14973898X-RAY DIFFRACTION100
4.27-4.440.15811660.14594014X-RAY DIFFRACTION100
4.44-4.650.20412100.14663947X-RAY DIFFRACTION100
4.65-4.890.1822060.14843936X-RAY DIFFRACTION100
4.89-5.20.22881800.15873984X-RAY DIFFRACTION100
5.2-5.60.1581590.15163977X-RAY DIFFRACTION99.9
5.6-6.160.21681930.17943958X-RAY DIFFRACTION100
6.16-7.050.22691860.19483970X-RAY DIFFRACTION100
7.05-8.880.21852130.20053947X-RAY DIFFRACTION100
8.88-62.70.20042260.18483915X-RAY DIFFRACTION99.57

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