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- PDB-7c3h: Structure of L-lysine oxidase in complex with L-lysine -

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Basic information

Entry
Database: PDB / ID: 7c3h
TitleStructure of L-lysine oxidase in complex with L-lysine
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 / LYSINE / L-Lysine alpha-oxidase / L-lysine oxidase
Similarity search - Component
Biological speciesHypocrea rufa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKondo, H. / Kitagawa, M. / Sugiyama, S. / Imada, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24560962 Japan
Japan Society for the Promotion of Science (JSPS)25286051 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)124,46212
Polymers121,7512
Non-polymers2,71010
Water16,538918
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-22 kcal/mol
Surface area35020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.110, 170.270, 119.490
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: 60875.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea rufa (fungus) / Strain: Y244-2 / Production host: Streptomyces lividans TK24 (bacteria)
References: UniProt: A0A0J9X1X3, UniProt: A0A0G4DCU0*PLUS, L-lysine oxidase

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Non-polymers , 5 types, 928 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-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / 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.: 918 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 7
Details: 4% (w/v) PEG 400, 0.1 M HEPES pH 7.0, 2.0 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 22, 2014
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→24 Å / Num. obs: 129154 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 12.33 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 18744

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Processing

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

3x0v


Resolution: 1.7→23.98 Å / SU ML: 0.1615 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 6453 5.02 %
Rwork0.1754 122009 -
obs0.177 128462 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.98 Å2
Refinement stepCycle: LAST / Resolution: 1.7→23.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8022 0 180 918 9120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01868551
X-RAY DIFFRACTIONf_angle_d1.437911638
X-RAY DIFFRACTIONf_chiral_restr0.0941217
X-RAY DIFFRACTIONf_plane_restr0.01041481
X-RAY DIFFRACTIONf_dihedral_angle_d5.1336784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.25322120.20684048X-RAY DIFFRACTION99.65
1.72-1.740.24852100.20584042X-RAY DIFFRACTION99.72
1.74-1.760.23261840.19614086X-RAY DIFFRACTION99.72
1.76-1.780.24782130.19674056X-RAY DIFFRACTION99.79
1.78-1.810.24782090.20574071X-RAY DIFFRACTION99.74
1.81-1.830.21942120.2034078X-RAY DIFFRACTION99.77
1.83-1.860.23982000.19784061X-RAY DIFFRACTION99.77
1.86-1.890.2452210.20854025X-RAY DIFFRACTION99.39
1.89-1.910.27852280.23693843X-RAY DIFFRACTION94.9
1.91-1.950.24742190.22173989X-RAY DIFFRACTION97.77
1.95-1.980.22982180.17794050X-RAY DIFFRACTION99.77
1.98-2.020.20272270.16594074X-RAY DIFFRACTION99.84
2.02-2.050.19782000.17374035X-RAY DIFFRACTION99.06
2.05-2.10.22652160.18674027X-RAY DIFFRACTION99.02
2.1-2.140.20582410.17434048X-RAY DIFFRACTION99.88
2.14-2.190.21492300.17084090X-RAY DIFFRACTION99.75
2.19-2.250.25942100.2023935X-RAY DIFFRACTION97
2.25-2.310.28091980.20143990X-RAY DIFFRACTION97.53
2.31-2.370.19852240.1674056X-RAY DIFFRACTION99.56
2.37-2.450.18422120.1674065X-RAY DIFFRACTION98.84
2.45-2.540.18712130.16094096X-RAY DIFFRACTION99.86
2.54-2.640.20861940.16624121X-RAY DIFFRACTION99.86
2.64-2.760.19642320.16844065X-RAY DIFFRACTION99.77
2.76-2.910.20822220.16724116X-RAY DIFFRACTION99.98
2.91-3.090.18852040.17064154X-RAY DIFFRACTION100
3.09-3.330.21172020.17534129X-RAY DIFFRACTION99.77
3.33-3.660.19331940.16454097X-RAY DIFFRACTION98.44
3.66-4.190.17162170.15064109X-RAY DIFFRACTION98.97
4.19-5.260.17972540.13924164X-RAY DIFFRACTION99.84
5.26-23.980.17942370.17354289X-RAY DIFFRACTION99.23

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