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- PDB-7c3j: Structure of L-lysine oxidase D212A/D315A in complex with L-pheny... -

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Basic information

Entry
Database: PDB / ID: 7c3j
TitleStructure of L-lysine oxidase D212A/D315A in complex with L-phenylalanine
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 / PHENYLALANINE / L-Lysine alpha-oxidase / L-lysine oxidase
Similarity search - Component
Biological speciesHypocrea rufa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)124,03712
Polymers121,5752
Non-polymers2,46210
Water11,656647
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-44 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.920, 169.680, 118.530
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, 657 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-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
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: Nov 23, 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: 2.2→95.2 Å / Num. obs: 58372 / % possible obs: 99.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.49 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4495 / % possible all: 98.7

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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: 2.2→68.99 Å / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.6653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 3004 5.16 %
Rwork0.1858 55260 -
obs0.1884 58264 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.07 Å2
Refinement stepCycle: LAST / Resolution: 2.2→68.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8074 0 164 647 8885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318482
X-RAY DIFFRACTIONf_angle_d0.635411541
X-RAY DIFFRACTIONf_chiral_restr0.0431213
X-RAY DIFFRACTIONf_plane_restr0.00481467
X-RAY DIFFRACTIONf_dihedral_angle_d5.14496774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.29321300.23312639X-RAY DIFFRACTION98.4
2.24-2.270.281420.2212590X-RAY DIFFRACTION98.59
2.27-2.320.24741270.21242541X-RAY DIFFRACTION97.12
2.32-2.360.2741420.21142518X-RAY DIFFRACTION95.86
2.36-2.410.29971280.21222606X-RAY DIFFRACTION98.17
2.41-2.460.23581470.20632624X-RAY DIFFRACTION98.89
2.46-2.520.22751380.19562610X-RAY DIFFRACTION99.24
2.52-2.580.24411660.19532600X-RAY DIFFRACTION99
2.58-2.650.26931410.2052622X-RAY DIFFRACTION99.14
2.65-2.730.30161530.19842602X-RAY DIFFRACTION99.49
2.73-2.820.29171400.19952648X-RAY DIFFRACTION99.43
2.82-2.920.251480.20262617X-RAY DIFFRACTION98.93
2.92-3.030.24721740.22605X-RAY DIFFRACTION99.21
3.03-3.170.26991430.19472639X-RAY DIFFRACTION99.29
3.17-3.340.21961500.18112614X-RAY DIFFRACTION98.5
3.34-3.550.24471420.17722618X-RAY DIFFRACTION97.91
3.55-3.820.17671400.15922684X-RAY DIFFRACTION99.58
3.82-4.210.18811320.14772669X-RAY DIFFRACTION99.72
4.21-4.820.20011480.14912688X-RAY DIFFRACTION99.86
4.82-6.070.20681380.18012749X-RAY DIFFRACTION99.9
6.07-68.990.22611350.19562777X-RAY DIFFRACTION97.65

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