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- PDB-7eii: Ancestral L-Lys oxidase K387A variant (L-Lys binding form) -

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Basic information

Entry
Database: PDB / ID: 7eii
TitleAncestral L-Lys oxidase K387A variant (L-Lys binding form)
ComponentsFAD dependent L-Lys oxidase
KeywordsOXIDOREDUCTASE / L-Lys oxidase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / LYSINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSugiura, S. / Nakano, S. / Niwa, M. / Hasebe, F. / Ito, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K18688 Japan
Japan Society for the Promotion of Science (JSPS)18K14391 Japan
Japan Science and TechnologyJPMJPR20AB Japan
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining.
Authors: Sugiura, S. / Nakano, S. / Niwa, M. / Hasebe, F. / Matsui, D. / Ito, S.
History
DepositionMar 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD dependent L-Lys oxidase
B: FAD dependent L-Lys oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,9855
Polymers137,2672
Non-polymers1,7183
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-26 kcal/mol
Surface area44640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.829, 80.086, 87.986
Angle α, β, γ (deg.)90.000, 90.425, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FAD dependent L-Lys oxidase


Mass: 68633.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / 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.: 369 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 25%(w/v) PEG3350, 0.1 M Tris-HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→42.9 Å / Num. obs: 46762 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.2
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.421 / Num. unique obs: 6740 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EIH

7eih


Resolution: 2.4→42.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.56 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / ESU R: 0.669 / ESU R Free: 0.267
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2308 2378 5.087 %
Rwork0.1828 44371 -
all0.185 --
obs-46749 99.806 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.645 Å20 Å21.747 Å2
2---1.198 Å20 Å2
3---0.528 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9495 0 116 369 9980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139886
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178998
X-RAY DIFFRACTIONr_angle_refined_deg1.461.64613428
X-RAY DIFFRACTIONr_angle_other_deg1.2821.58120797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72151167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12423.957508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.839151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2651532
X-RAY DIFFRACTIONr_chiral_restr0.070.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022306
X-RAY DIFFRACTIONr_nbd_refined0.2070.22095
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.28779
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24697
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.24446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2502
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0680.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1560.29
X-RAY DIFFRACTIONr_nbd_other0.2210.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.28
X-RAY DIFFRACTIONr_mcbond_it2.7783.6284680
X-RAY DIFFRACTIONr_mcbond_other2.7783.6274679
X-RAY DIFFRACTIONr_mcangle_it4.3015.4325843
X-RAY DIFFRACTIONr_mcangle_other4.3015.4335844
X-RAY DIFFRACTIONr_scbond_it2.9533.9085206
X-RAY DIFFRACTIONr_scbond_other2.9533.9095203
X-RAY DIFFRACTIONr_scangle_it4.7095.7487585
X-RAY DIFFRACTIONr_scangle_other4.7095.7477586
X-RAY DIFFRACTIONr_lrange_it7.28641.28211526
X-RAY DIFFRACTIONr_lrange_other7.28441.22111467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.2891800.2293189X-RAY DIFFRACTION98.0215
2.462-2.530.3131650.2233199X-RAY DIFFRACTION100
2.53-2.6030.2871920.2163076X-RAY DIFFRACTION100
2.603-2.6830.3271720.2132995X-RAY DIFFRACTION100
2.683-2.7710.2931440.2082935X-RAY DIFFRACTION100
2.771-2.8680.2621370.2032846X-RAY DIFFRACTION100
2.868-2.9760.2221550.1942706X-RAY DIFFRACTION100
2.976-3.0980.271440.2072603X-RAY DIFFRACTION100
3.098-3.2350.2671260.22520X-RAY DIFFRACTION100
3.235-3.3930.217990.1982456X-RAY DIFFRACTION100
3.393-3.5760.2511050.1912316X-RAY DIFFRACTION100
3.576-3.7930.226940.1852200X-RAY DIFFRACTION100
3.793-4.0540.201970.1532052X-RAY DIFFRACTION100
4.054-4.3780.1921270.1381881X-RAY DIFFRACTION100
4.378-4.7950.1881080.1411743X-RAY DIFFRACTION100
4.795-5.3590.198720.1551625X-RAY DIFFRACTION100
5.359-6.1840.229790.1781408X-RAY DIFFRACTION100
6.184-7.5640.295700.1761182X-RAY DIFFRACTION100
7.564-10.6580.141990.145903X-RAY DIFFRACTION99.9003
10.658-42.950.158130.229536X-RAY DIFFRACTION96.3158

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