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- PDB-7d4e: Structure of L-lysine oxidase precursor in complex with L-lysine ... -

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Basic information

Entry
Database: PDB / ID: 7d4e
TitleStructure of L-lysine oxidase precursor in complex with L-lysine (1.0 M)
ComponentsL-Lysine alpha-oxidase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesHypocrea rufa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKitagawa, M. / Ito, N. / Matsumoto, Y. / Inagaki, K. / Imada, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24560962 Japan
CitationJournal: J Struct Biol X / Year: 2021
Title: Structural basis of enzyme activity regulation by the propeptide of l-lysine alpha-oxidase precursor from Trichoderma viride .
Authors: Kitagawa, M. / Ito, N. / Matsumoto, Y. / Saito, M. / Tamura, T. / Kusakabe, H. / Inagaki, K. / Imada, K.
History
DepositionSep 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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

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Assembly

Deposited unit
A: L-Lysine alpha-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5023
Polymers69,5701
Non-polymers9332
Water7,728429
1
A: L-Lysine alpha-oxidase
hetero molecules

A: L-Lysine alpha-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0056
Polymers139,1392
Non-polymers1,8654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8150 Å2
ΔGint-24 kcal/mol
Surface area41810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.889, 130.050, 94.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-940-

HOH

21A-941-

HOH

31A-994-

HOH

41A-1002-

HOH

51A-1135-

HOH

61A-1164-

HOH

71A-1186-

HOH

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Components

#1: Protein L-Lysine alpha-oxidase


Mass: 69569.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea rufa (fungus) / Gene: LysOX / Plasmid: pCold IV / Production host: Escherichia coli (E. coli) / Strain (production host): Solu BL21 / References: UniProt: A0A0G4DCU0
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl pH8.0 (-9.0) and 2.1 M ammonium dihydrogen phosphate

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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 PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2017
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→76.7 Å / Num. obs: 49629 / % possible obs: 99.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.028 / Net I/σ(I): 16.9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4 / Num. unique obs: 3015 / CC1/2: 0.902 / Rpim(I) all: 0.186 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
BSSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3x0v

3x0v


Resolution: 1.85→65.025 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2558 5.16 %
Rwork0.1648 --
obs0.1669 49596 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→65.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 63 429 5089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195324
X-RAY DIFFRACTIONf_angle_d1.6317249
X-RAY DIFFRACTIONf_dihedral_angle_d8.7213942
X-RAY DIFFRACTIONf_chiral_restr0.098763
X-RAY DIFFRACTIONf_plane_restr0.011938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88560.30161600.21342560X-RAY DIFFRACTION99
1.8856-1.92410.23481540.20342544X-RAY DIFFRACTION98
1.9241-1.96590.24431520.19422578X-RAY DIFFRACTION99
1.9659-2.01170.21531490.18292556X-RAY DIFFRACTION99
2.0117-2.0620.25661620.1782587X-RAY DIFFRACTION99
2.062-2.11770.22271530.17072549X-RAY DIFFRACTION99
2.1177-2.18010.20661340.17082595X-RAY DIFFRACTION99
2.1801-2.25040.24551250.16372620X-RAY DIFFRACTION99
2.2504-2.33090.20571410.15782573X-RAY DIFFRACTION99
2.3309-2.42420.22421460.15132568X-RAY DIFFRACTION98
2.4242-2.53450.19411350.1532628X-RAY DIFFRACTION99
2.5345-2.66820.18641290.16392625X-RAY DIFFRACTION100
2.6682-2.83530.25331260.1642632X-RAY DIFFRACTION100
2.8353-3.05420.22871480.16622633X-RAY DIFFRACTION99
3.0542-3.36160.20671160.16172670X-RAY DIFFRACTION99
3.3616-3.8480.17551430.14212632X-RAY DIFFRACTION99
3.848-4.84780.15921380.13572684X-RAY DIFFRACTION100
4.8478-65.0250.18861470.20222804X-RAY DIFFRACTION99

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