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- PDB-7f1y: L-lactate oxidase without substrate -

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Basic information

Entry
Database: PDB / ID: 7f1y
TitleL-lactate oxidase without substrate
ComponentsLactate oxidase
KeywordsOXIDOREDUCTASE / L-lactate / complex
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor / FMN binding / oxidoreductase activity / metal ion binding
Similarity search - Function
L-lactate oxidase / Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / L-lactate oxidase
Similarity search - Component
Biological speciesAerococcus viridans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMorimoto, Y. / Inaka, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Dynamic interactions in the l-lactate oxidase active site facilitate substrate binding at pH4.5.
Authors: Furubayashi, N. / Inaka, K. / Kamo, M. / Umena, Y. / Matsuoka, T. / Morimoto, Y.
History
DepositionJun 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactate oxidase
B: Lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7418
Polymers80,5862
Non-polymers1,1556
Water13,115728
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.298, 132.298, 91.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-799-

HOH

21A-812-

HOH

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Components

#1: Protein Lactate oxidase


Mass: 40293.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus viridans (bacteria) / Production host: Aerococcus viridans (bacteria) / References: UniProt: Q44467
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 20 mg/ml in 50 mM sodium acetate (pH4.5) , 40% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.33→45.66 Å / Num. obs: 167253 / % possible obs: 98.38 % / Redundancy: 20 % / CC1/2: 0.984 / Net I/σ(I): 15.76
Reflection shellResolution: 1.33→1.38 Å / Num. unique obs: 16501 / CC1/2: 0.659

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DU2

2du2


Resolution: 1.33→45.66 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.922 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19261 8622 4.9 %RANDOM
Rwork0.17036 ---
obs0.17142 167253 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.944 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.64 Å2
Refinement stepCycle: 1 / Resolution: 1.33→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5547 0 78 729 6354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135755
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175237
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.6427803
X-RAY DIFFRACTIONr_angle_other_deg1.5361.57912135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33822.392301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72515914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7971536
X-RAY DIFFRACTIONr_chiral_restr0.1080.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021216
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.452.5072877
X-RAY DIFFRACTIONr_mcbond_other2.452.5072875
X-RAY DIFFRACTIONr_mcangle_it3.8973.7483585
X-RAY DIFFRACTIONr_mcangle_other3.8973.7473586
X-RAY DIFFRACTIONr_scbond_it3.8322.9522878
X-RAY DIFFRACTIONr_scbond_other3.8322.9532879
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8514.264219
X-RAY DIFFRACTIONr_long_range_B_refined19.3535.117513
X-RAY DIFFRACTIONr_long_range_B_other19.3535.1097513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.332→1.367 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 638 -
Rwork0.293 11328 -
obs--90.64 %

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