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- PDB-7c3i: Structure of L-lysine oxidase D212A/D315A -

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Basic information

Entry
Database: PDB / ID: 7c3i
TitleStructure of L-lysine oxidase D212A/D315A
ComponentsL-lysine oxidase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase
Function / homology
Function and homology information


L-lysine oxidase activity / L-lysine oxidase / L-amino-acid oxidase activity / amino acid catabolic process / nucleotide binding
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / L-Lysine alpha-oxidase / L-lysine oxidase
Similarity search - Component
Biological speciesHypocrea rufa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKitagawa, M. / Matsumoto, Y. / Inagaki, K. / Imada, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24560962 Japan
CitationJournal: Protein Sci. / Year: 2020
Title: Structural basis of strict substrate recognition of l-lysine alpha-oxidase from Trichoderma viride.
Authors: Kondo, H. / Kitagawa, M. / Matsumoto, Y. / Saito, M. / Amano, M. / Sugiyama, S. / Tamura, T. / Kusakabe, H. / Inagaki, K. / Imada, K.
History
DepositionMay 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lysine oxidase
B: L-lysine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,99910
Polymers121,5752
Non-polymers2,4248
Water12,791710
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-34 kcal/mol
Surface area37080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.450, 170.291, 119.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-lysine oxidase


Mass: 60787.598 Da / Num. of mol.: 2 / Mutation: D212A, D315A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea rufa (fungus) / Plasmid: pCold IV / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21
References: UniProt: A0A0J9X1X3, UniProt: A0A0G4DCU0*PLUS, L-lysine oxidase

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Non-polymers , 5 types, 718 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1% (w/v) PEG 400, 0.1 M Tris-HCl pH 7.5, 2.1 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2018
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→85.2 Å / Num. obs: 52760 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.85 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.37 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 4537

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X0V

3x0v


Resolution: 2.3→74.91 Å / SU ML: 0.2126 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.6013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 2665 5.08 %
Rwork0.1787 49803 -
obs0.1811 52468 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.94 Å2
Refinement stepCycle: LAST / Resolution: 2.3→74.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7998 0 158 710 8866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00468406
X-RAY DIFFRACTIONf_angle_d0.705911436
X-RAY DIFFRACTIONf_chiral_restr0.04541200
X-RAY DIFFRACTIONf_plane_restr0.00451444
X-RAY DIFFRACTIONf_dihedral_angle_d6.37196708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.25471570.20792610X-RAY DIFFRACTION99.93
2.34-2.390.27511730.19772578X-RAY DIFFRACTION99.82
2.39-2.440.26861450.18182591X-RAY DIFFRACTION100
2.44-2.490.26591310.18362631X-RAY DIFFRACTION99.78
2.49-2.550.22321250.18112630X-RAY DIFFRACTION99.93
2.55-2.610.22861140.18242636X-RAY DIFFRACTION99.85
2.61-2.680.3121230.18692646X-RAY DIFFRACTION99.89
2.68-2.760.23191440.1862623X-RAY DIFFRACTION99.78
2.76-2.850.28011410.19342619X-RAY DIFFRACTION99.21
2.85-2.950.22641470.18992603X-RAY DIFFRACTION99.53
2.95-3.070.22361700.18042595X-RAY DIFFRACTION99.42
3.07-3.210.23521480.19062586X-RAY DIFFRACTION98.24
3.21-3.380.21281230.17682591X-RAY DIFFRACTION98.33
3.38-3.590.21241440.17582674X-RAY DIFFRACTION99.86
3.59-3.870.26191200.19912489X-RAY DIFFRACTION93.31
3.87-4.260.17681410.1522623X-RAY DIFFRACTION98.4
4.26-4.870.17751410.14622674X-RAY DIFFRACTION99.79
4.87-6.140.22991370.17192693X-RAY DIFFRACTION99.05
6.14-74.910.17671410.17762711X-RAY DIFFRACTION96.35

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