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- PDB-7x7j: Ancestral L-Lys oxidase (AncLLysO-2) L-Lys binding form -

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Basic information

Entry
Database: PDB / ID: 7x7j
TitleAncestral L-Lys oxidase (AncLLysO-2) L-Lys binding form
ComponentsFAD dependent enzyme
KeywordsOXIDOREDUCTASE / L-Lys oxidase / Ancestral Sequence Reconstruction / L-Lys binding form
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / LYSINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMotoyama, T. / Ishida, C. / Hasebe, F. / Ito, S. / Nakano, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR20AB Japan
Japan Society for the Promotion of Science (JSPS)21K05395 Japan
Japan Society for the Promotion of Science (JSPS)19J23697 Japan
CitationJournal: Acs Omega / Year: 2022
Title: Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis
Authors: Motoyama, T. / Yamamoto, Y. / Ishida, C. / Hasebe, F. / Kawamura, Y. / Shigeta, Y. / Ito, S. / Nakano, S.
History
DepositionMar 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD dependent enzyme
B: FAD dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,1886
Polymers130,3222
Non-polymers1,8654
Water29,2021621
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-43 kcal/mol
Surface area37700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.408, 77.400, 93.414
Angle α, β, γ (deg.)90.000, 104.365, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FAD dependent enzyme


Mass: 65161.125 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.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1621 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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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: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→45.3 Å / Num. obs: 215621 / % possible obs: 99.1 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 27.2
Reflection shellResolution: 1.4→1.47 Å / Num. unique obs: 29666 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X7I

7x7i


Resolution: 1.4→45.3 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.999 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.183 10663 4.946 %
Rwork0.158 204929 -
all0.159 --
obs-215621 99.1 %
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: 15.786 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9024 0 126 1621 10771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0139424
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178104
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.64712922
X-RAY DIFFRACTIONr_angle_other_deg1.6181.56618796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70951164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20823.266496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.227151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.211542
X-RAY DIFFRACTIONr_chiral_restr0.10.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0210856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022048
X-RAY DIFFRACTIONr_nbd_refined0.2220.21964
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.27974
X-RAY DIFFRACTIONr_nbtor_refined0.1860.24777
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.24048
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.21147
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1280.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.210
X-RAY DIFFRACTIONr_nbd_other0.1870.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0350.21
X-RAY DIFFRACTIONr_mcbond_it1.6751.5094668
X-RAY DIFFRACTIONr_mcbond_other1.6741.5094667
X-RAY DIFFRACTIONr_mcangle_it2.5392.2655828
X-RAY DIFFRACTIONr_mcangle_other2.5392.2665829
X-RAY DIFFRACTIONr_scbond_it2.3011.6494756
X-RAY DIFFRACTIONr_scbond_other2.2971.6494756
X-RAY DIFFRACTIONr_scangle_it3.4182.4157094
X-RAY DIFFRACTIONr_scangle_other3.4142.4157094
X-RAY DIFFRACTIONr_lrange_it5.38119.97411603
X-RAY DIFFRACTIONr_lrange_other5.03418.66311039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4310.2917080.27613528X-RAY DIFFRACTION88.8473
1.431-1.470.2477570.23114664X-RAY DIFFRACTION98.625
1.47-1.5130.2327710.21214432X-RAY DIFFRACTION100
1.513-1.5590.2417360.19214030X-RAY DIFFRACTION99.9865
1.559-1.610.2167500.17713576X-RAY DIFFRACTION100
1.61-1.6670.2026870.17313174X-RAY DIFFRACTION100
1.667-1.730.2046700.16612709X-RAY DIFFRACTION100
1.73-1.80.2086050.15912251X-RAY DIFFRACTION100
1.8-1.880.1756400.15411740X-RAY DIFFRACTION100
1.88-1.9720.1875780.15511203X-RAY DIFFRACTION100
1.972-2.0790.1795640.15510681X-RAY DIFFRACTION100
2.079-2.2050.175090.14910169X-RAY DIFFRACTION100
2.205-2.3570.1654720.149479X-RAY DIFFRACTION100
2.357-2.5450.1614360.1358897X-RAY DIFFRACTION100
2.545-2.7880.184210.1448175X-RAY DIFFRACTION100
2.788-3.1170.1613780.1447425X-RAY DIFFRACTION100
3.117-3.5980.1593270.146533X-RAY DIFFRACTION100
3.598-4.4050.1563200.1345523X-RAY DIFFRACTION100
4.405-6.2230.1972290.1824309X-RAY DIFFRACTION100
6.223-45.2880.1831050.1582431X-RAY DIFFRACTION99.2175

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