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- PDB-7d4c: Structure of L-lysine oxidase precursor -

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Basic information

Entry
Database: PDB / ID: 7d4c
TitleStructure of L-lysine oxidase precursor
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 / PHOSPHATE ION / L-Lysine alpha-oxidase
Similarity search - Component
Biological speciesHypocrea rufa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsIto, N. / Kitagawa, M. / 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)70,6405
Polymers69,5701
Non-polymers1,0704
Water10,269570
1
A: L-Lysine alpha-oxidase
hetero molecules

A: L-Lysine alpha-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,28010
Polymers139,1392
Non-polymers2,1418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9670 Å2
ΔGint-52 kcal/mol
Surface area44280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.160, 130.920, 94.070
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-1018-

HOH

21A-1035-

HOH

31A-1054-

HOH

41A-1113-

HOH

51A-1216-

HOH

61A-1269-

HOH

71A-1415-

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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH8.5 and 2.0 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: Apr 19, 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: 1.97→94.1 Å / Num. obs: 39115 / % possible obs: 93.5 % / Redundancy: 5 % / Biso Wilson estimate: 13 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2880 / CC1/2: 0.81 / Rpim(I) all: 0.284 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
BSSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X0V

3x0v


Resolution: 1.97→76.975 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 1890 4.92 %
Rwork0.2028 --
obs0.2044 38412 91.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→76.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 68 570 5361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034931
X-RAY DIFFRACTIONf_angle_d0.8216710
X-RAY DIFFRACTIONf_dihedral_angle_d14.1011795
X-RAY DIFFRACTIONf_chiral_restr0.03708
X-RAY DIFFRACTIONf_plane_restr0.005859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.01930.26881440.23042762X-RAY DIFFRACTION100
2.0193-2.07390.27521390.22072603X-RAY DIFFRACTION100
2.0739-2.13490.26361130.20662222X-RAY DIFFRACTION100
2.1349-2.20380.24141490.22352814X-RAY DIFFRACTION100
2.2038-2.28260.5569710.45131387X-RAY DIFFRACTION50
2.2826-2.3740.26941410.21442855X-RAY DIFFRACTION100
2.374-2.4820.25391520.20122802X-RAY DIFFRACTION100
2.482-2.61290.23111300.20272841X-RAY DIFFRACTION100
2.6129-2.77660.24261260.19782427X-RAY DIFFRACTION86
2.7766-2.9910.22731440.20512830X-RAY DIFFRACTION100
2.991-3.2920.20911590.19072839X-RAY DIFFRACTION100
3.292-3.76840.25331150.18692430X-RAY DIFFRACTION84
3.7684-4.74760.19441580.15932711X-RAY DIFFRACTION94
4.7476-76.9750.1711490.18862999X-RAY DIFFRACTION100

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