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- PDB-7d4d: Structure of L-lysine oxidase precursor in complex with L-lysine ... -

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Basic information

Entry
Database: PDB / ID: 7d4d
TitleStructure of L-lysine oxidase precursor in complex with L-lysine (1.24M)
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: 2.29 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
Water3,477193
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 area8680 Å2
ΔGint-20 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.310, 127.960, 94.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
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
Components on special symmetry positions
IDModelComponents
11A-934-

HOH

21A-1024-

HOH

31A-1054-

HOH

41A-1079-

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: isolated from a natural source / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCl pH8.0 and 2.1 M Potassium 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 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: 2.29→94.4 Å / Num. obs: 25914 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 32.17 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.056 / Net I/σ(I): 12.9
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2533 / CC1/2: 0.861 / Rpim(I) all: 0.304 / % possible all: 99.6

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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: 2.29→75.918 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 1261 4.87 %
Rwork0.1692 --
obs0.1717 25885 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→75.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 63 193 4280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084201
X-RAY DIFFRACTIONf_angle_d0.9255712
X-RAY DIFFRACTIONf_dihedral_angle_d6.0592433
X-RAY DIFFRACTIONf_chiral_restr0.05602
X-RAY DIFFRACTIONf_plane_restr0.006726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.38170.28651430.22422709X-RAY DIFFRACTION99
2.3817-2.49010.28351450.20622710X-RAY DIFFRACTION100
2.4901-2.62140.24561260.1912722X-RAY DIFFRACTION100
2.6214-2.78570.25331220.18822715X-RAY DIFFRACTION99
2.7857-3.00080.27281450.18562697X-RAY DIFFRACTION99
3.0008-3.30270.2531520.17052737X-RAY DIFFRACTION100
3.3027-3.78060.18431310.15292757X-RAY DIFFRACTION100
3.7806-4.76310.19111440.14352733X-RAY DIFFRACTION98
4.7631-75.9180.18941530.16462844X-RAY DIFFRACTION99

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