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- PDB-3x0v: Structure of L-lysine oxidase -

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Basic information

Entry
Database: PDB / ID: 3x0v
TitleStructure of L-lysine oxidase
ComponentsL-lysine oxidase
KeywordsOXIDOREDUCTASE / oxidative deamination / secreted protein
Function / homology
Function and homology information


L-lysine oxidase activity / L-lysine oxidase / 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 oxidase
Similarity search - Component
Biological speciesTrichoderma viride (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSano, T. / Uchida, Y. / Amano, M. / Kawaguchi, T. / Kondo, H. / Inagaki, K. / Imada, K.
CitationJournal: J.Biochem. / Year: 2015
Title: Recombinant expression, molecular characterization and crystal structure of antitumor enzyme, l-lysine alpha-oxidase from Trichoderma viride.
Authors: Amano, M. / Mizuguchi, H. / Sano, T. / Kondo, H. / Shinyashiki, K. / Inagaki, J. / Tamura, T. / Kawaguchi, T. / Kusakabe, H. / Imada, K. / Inagaki, K.
History
DepositionOct 22, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)124,4748
Polymers121,9492
Non-polymers2,5246
Water14,160786
1
A: L-lysine oxidase
hetero molecules

A: L-lysine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4748
Polymers121,9492
Non-polymers2,5246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10370 Å2
ΔGint-5 kcal/mol
Surface area37180 Å2
MethodPISA
2
B: L-lysine oxidase
hetero molecules

B: L-lysine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4748
Polymers121,9492
Non-polymers2,5246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10310 Å2
ΔGint-5 kcal/mol
Surface area37130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.975, 170.012, 81.046
Angle α, β, γ (deg.)90.00, 132.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-723-

HOH

21A-1064-

HOH

31B-802-

HOH

41B-1036-

HOH

51B-1056-

HOH

61B-1058-

HOH

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Components

#1: Protein L-lysine oxidase


Mass: 60974.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichoderma viride (fungus) / Strain: Y244-2 / References: UniProt: A0A0J9X1X3*PLUS, L-lysine oxidase
#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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 2% (w/v) PEG 400, 0.1M HEPES pH7.6, 1.8M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 19, 2012
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→34.4 Å / Num. all: 92177 / Num. obs: 92177 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.4 / Num. unique all: 13448 / % possible all: 100

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Processing

Software
NameVersionClassification
SPring-8BBSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KVE

3kve


Resolution: 1.9→32.023 Å / SU ML: 0.4 / σ(F): 1.4 / Phase error: 17.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 4613 5 %RANDOM
Rwork0.1588 ---
obs0.1603 92171 99.96 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.23 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6639 Å20 Å2-0.4098 Å2
2---0.2063 Å2-0 Å2
3---0.8702 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8086 0 166 786 9038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078486
X-RAY DIFFRACTIONf_angle_d1.24311548
X-RAY DIFFRACTIONf_dihedral_angle_d12.0483086
X-RAY DIFFRACTIONf_chiral_restr0.1041208
X-RAY DIFFRACTIONf_plane_restr0.0071462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.24551570.20752926100
1.9216-1.94420.25781530.19942914100
1.9442-1.96790.26041510.19472906100
1.9679-1.99280.20021380.17872905100
1.9928-2.0190.21981380.16542972100
2.019-2.04670.22481360.16412936100
2.0467-2.07590.1951630.16472898100
2.0759-2.10690.23431390.16392897100
2.1069-2.13980.20061680.16592895100
2.1398-2.17490.22191670.1642914100
2.1749-2.21240.20961510.16282901100
2.2124-2.25260.2091670.16282928100
2.2526-2.29590.18441560.15842907100
2.2959-2.34280.19771730.15532872100
2.3428-2.39370.20751560.15462931100
2.3937-2.44940.19741530.15732914100
2.4494-2.51060.21271680.15762888100
2.5106-2.57840.17971600.15192917100
2.5784-2.65430.19771510.15292925100
2.6543-2.73990.20831710.16452897100
2.7399-2.83780.21891490.16032911100
2.8378-2.95130.20841430.17452935100
2.9513-3.08550.18371440.16892935100
3.0855-3.24810.19331510.17292942100
3.2481-3.45130.17821380.15442941100
3.4513-3.71750.13411610.14322906100
3.7175-4.09090.13911320.1372942100
4.0909-4.68130.13851620.12492931100
4.6813-5.89190.1711590.15192930100
5.8919-32.02740.18161580.1727294299

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