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- PDB-7f22: L-lactate oxidase with pyruvate -

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Basic information

Entry
Database: PDB / ID: 7f22
TitleL-lactate oxidase with pyruvate
ComponentsL-lactate oxidase
KeywordsOXIDOREDUCTASE / pyruvate / complex
Function / homologyFLAVIN MONONUCLEOTIDE / PYRUVIC ACID
Function and homology information
Biological speciesAerococcus viridans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-lactate oxidase
B: L-lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,2256
Polymers161,1372
Non-polymers1,0894
Water13,331740
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)132.604, 132.604, 91.766
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-1207-

HOH

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Components

#1: Protein L-lactate oxidase


Mass: 80568.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus viridans (bacteria) / Production host: Aerococcus viridans (bacteria)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 1.25 Å3/Da / Density % sol: 1.74 %
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: 1.41→46.93 Å / Num. obs: 143078 / % possible obs: 99.75 % / Redundancy: 17.6 % / CC1/2: 0.963 / Net I/σ(I): 16.75
Reflection shellResolution: 1.41→1.464 Å / Num. unique obs: 14714 / CC1/2: 0.591

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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: 1.41→46.93 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.161 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21608 7774 5.2 %RANDOM
Rwork0.19337 ---
obs0.19455 143078 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.871 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.41→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5682 0 74 740 6496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135886
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175356
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.6417986
X-RAY DIFFRACTIONr_angle_other_deg1.5191.57912412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6895734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75122.244312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93515942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8081538
X-RAY DIFFRACTIONr_chiral_restr0.0980.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021250
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_it2.7912.5882942
X-RAY DIFFRACTIONr_mcbond_other2.7922.5882941
X-RAY DIFFRACTIONr_mcangle_it4.323.8813674
X-RAY DIFFRACTIONr_mcangle_other4.3193.8813675
X-RAY DIFFRACTIONr_scbond_it2.8422.792944
X-RAY DIFFRACTIONr_scbond_other2.8422.792945
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3124.084313
X-RAY DIFFRACTIONr_long_range_B_refined11.07733.197566
X-RAY DIFFRACTIONr_long_range_B_other10.84132.4187325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.414→1.451 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 518 -
Rwork0.369 10396 -
obs--97.51 %

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