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- PDB-7y8c: Crystal structure of CotA laccase complexed with syringaldehyde -

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Basic information

Entry
Database: PDB / ID: 7y8c
TitleCrystal structure of CotA laccase complexed with syringaldehyde
ComponentsSpore coat protein A
KeywordsOXIDOREDUCTASE / laccase
Function / homology
Function and homology information


bilirubin oxidase / laccase / sporulation resulting in formation of a cellular spore / outer membrane-bounded periplasmic space / oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / 3,5-dimethoxy-4-oxidanyl-benzaldehyde / TRIETHYLENE GLYCOL / Laccase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, Z.C. / Xie, T. / Wang, G.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Molecular insights into substrate promiscuity of CotA laccase catalyzing lignin-phenol derivatives.
Authors: Li, J. / Liu, Z. / Zhao, J. / Wang, G. / Xie, T.
History
DepositionJun 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spore coat protein A
B: Spore coat protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,99012
Polymers117,1502
Non-polymers84110
Water12,484693
1
A: Spore coat protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8295
Polymers58,5751
Non-polymers2544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spore coat protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1617
Polymers58,5751
Non-polymers5876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.329, 119.344, 84.088
Angle α, β, γ (deg.)90.000, 93.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spore coat protein A


Mass: 58574.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: cotA, pig, BSU06300 / Production host: Escherichia coli (E. coli) / References: UniProt: P07788
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-IJV / 3,5-dimethoxy-4-oxidanyl-benzaldehyde / Syringaldehyde


Mass: 182.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12-15.5% PEG 3350, 0.1M MgCl2, 0.1M pH 6.5 Bis-tris, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→48.6 Å / Num. obs: 70329 / % possible obs: 99.4 % / Redundancy: 4.4 % / CC1/2: 0.983 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5420 / CC1/2: 0.875

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q89

4q89


Resolution: 2→43.85 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 3485 4.96 %
Rwork0.1716 66777 -
obs0.1739 70262 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.63 Å2 / Biso mean: 32.5442 Å2 / Biso min: 12.92 Å2
Refinement stepCycle: final / Resolution: 2→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 41 693 8670
Biso mean--40.93 36.49 -
Num. residues----986
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.31861440.22992631277599
2.03-2.060.2621560.221127012857100
2.06-2.090.27181320.21992630276299
2.09-2.120.26951450.217726692814100
2.12-2.150.28451540.212626602814100
2.15-2.190.28151300.204626612791100
2.19-2.230.24451120.19662714282699
2.23-2.270.25991370.20462657279499
2.27-2.320.24121540.19762676283099
2.32-2.370.27041300.196926452775100
2.37-2.430.26371500.192327052855100
2.43-2.490.25851330.202626442777100
2.49-2.550.24461230.198727232846100
2.55-2.630.26791590.18926582817100
2.63-2.710.26731420.19872653279599
2.71-2.810.29481160.19372673278998
2.81-2.920.21931250.19142669279499
2.92-3.060.23291510.185326542805100
3.06-3.220.21691510.180226952846100
3.22-3.420.23621620.1722631279399
3.42-3.680.18761390.16072643278298
3.68-4.050.18371460.14112701284799
4.05-4.640.15761320.12312692282499
4.64-5.840.15741350.12952656279198
5.84-43.850.18771270.16192736286398

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