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- PDB-9nji: M298L Streptomyces coelicolor Laccase -

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Basic information

Entry
Database: PDB / ID: 9nji
TitleM298L 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
COPPER (II) ION / GLYCINE / HYDROXIDE ION / Copper oxidase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, J.-X. / Lu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Chem Sci / Year: 2025
Title: Unexpected effect of an axial ligand mutation in the type 1 copper center in small laccase: structure-based analyses and engineering to increase reduction potential and activity.
Authors: Wang, J.X. / Vilbert, A.C. / Williams, L.H. / Mirts, E.N. / Cui, C. / Lu, Y.
History
DepositionFeb 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 2, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,94512
Polymers37,9851
Non-polymers96011
Water2,828157
1
A: Copper oxidase
hetero molecules

A: Copper oxidase
hetero molecules

A: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,83536
Polymers113,9553
Non-polymers2,88033
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPISA
Unit cell
Length a, b, c (Å)177.228, 177.228, 177.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Copper oxidase


Mass: 37985.109 Da / Num. of mol.: 1 / Mutation: M298L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO6712, SC4C6.22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XAL8

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Non-polymers , 5 types, 168 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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, 0.5 M NaCl, pH 9.0, and 37-40% (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 week.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→44.31 Å / Num. obs: 29840 / % possible obs: 99.95 % / Redundancy: 40.5 % / Biso Wilson estimate: 50.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2881 / Rrim(I) all: 0.2917 / Net I/σ(I): 13.83
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 41.3 % / Rmerge(I) obs: 2.191 / Mean I/σ(I) obs: 1.76 / Num. unique obs: 2930 / CC1/2: 0.773 / Rrim(I) all: 2.218 / % possible all: 100

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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: 2.6→44.31 Å / SU ML: 0.3101 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.9341
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2016 2673 4.83 %
Rwork0.1856 52651 -
obs0.1864 29837 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.85 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 51 157 2358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222252
X-RAY DIFFRACTIONf_angle_d0.48413041
X-RAY DIFFRACTIONf_chiral_restr0.0459311
X-RAY DIFFRACTIONf_plane_restr0.0042401
X-RAY DIFFRACTIONf_dihedral_angle_d7.2239322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.31781510.32452794X-RAY DIFFRACTION100
2.65-2.70.33261540.29542737X-RAY DIFFRACTION100
2.7-2.750.23851320.25222789X-RAY DIFFRACTION100
2.75-2.810.2741480.24042792X-RAY DIFFRACTION100
2.81-2.880.23981230.21542740X-RAY DIFFRACTION100
2.88-2.950.21411450.21162796X-RAY DIFFRACTION100
2.95-3.030.19451870.18922704X-RAY DIFFRACTION100
3.03-3.120.22531460.18992752X-RAY DIFFRACTION100
3.12-3.220.21791320.18872818X-RAY DIFFRACTION99.93
3.22-3.340.24511360.18542760X-RAY DIFFRACTION100
3.34-3.470.15171630.15942708X-RAY DIFFRACTION100
3.47-3.630.13861340.14572801X-RAY DIFFRACTION100
3.63-3.820.16781090.15812778X-RAY DIFFRACTION100
3.82-4.060.181650.16982771X-RAY DIFFRACTION100
4.06-4.370.15911160.15282779X-RAY DIFFRACTION100
4.37-4.810.1791250.15642791X-RAY DIFFRACTION100
4.81-5.50.21491350.16482780X-RAY DIFFRACTION100
5.51-6.920.25341240.20772778X-RAY DIFFRACTION100
6.93-44.310.20311480.2332783X-RAY DIFFRACTION99.83

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