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- PDB-6r9v: Crystal structure of Pediococcus acidilactici lactate oxidase A94... -

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Basic information

Entry
Database: PDB / ID: 6r9v
TitleCrystal structure of Pediococcus acidilactici lactate oxidase A94G mutant
ComponentsPutative L-lactate oxidase
KeywordsOXIDOREDUCTASE / TIM Barrel / FMN / alpha hydroxyacid.
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
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 class I / Aldolase-type TIM barrel / TIM Barrel ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / L-lactate oxidase
Similarity search - Component
Biological speciesPediococcus acidilactici DSM 20284 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAshok, Y. / Maksimainen, M.M. / Lehtio, L.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Plos One / Year: 2020
Title: FMN-dependent oligomerization of putative lactate oxidase from Pediococcus acidilactici.
Authors: Ashok, Y. / Maksimainen, M.M. / Kallio, T. / Kilpelainen, P. / Lehtio, L.
History
DepositionApr 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 1, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.3Jan 24, 2024Group: 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: Putative L-lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5405
Polymers39,7051
Non-polymers8354
Water4,252236
1
A: Putative L-lactate oxidase
hetero molecules

A: Putative L-lactate oxidase
hetero molecules

A: Putative L-lactate oxidase
hetero molecules

A: Putative L-lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,15820
Polymers158,8194
Non-polymers3,33916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area16930 Å2
ΔGint-89 kcal/mol
Surface area48800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.530, 135.530, 124.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-639-

HOH

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Components

#1: Protein Putative L-lactate oxidase


Mass: 39704.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus acidilactici DSM 20284 (bacteria)
Gene: lctO, HMPREF0623_0568 / Production host: Escherichia coli (E. coli)
References: UniProt: E0NE46, Oxidoreductases; Acting on the CH-OH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M Sodium Malonate, 0.1M Hepes pH 7.0, 0.5% Jeffamine ED-2003.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39425 / % possible obs: 100 % / Redundancy: 13.2 % / Net I/σ(I): 11.98
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2879

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J6X

2j6x


Resolution: 2→45.92 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.994 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17512 1972 5 %RANDOM
Rwork0.15186 ---
obs0.15306 37453 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å2-0 Å2
2---1.32 Å20 Å2
3---2.65 Å2
Refinement stepCycle: 1 / Resolution: 2→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 56 236 3078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132906
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172714
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.6513933
X-RAY DIFFRACTIONr_angle_other_deg1.4031.5826320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61124.317139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98815488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3711512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02547
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_it1.6262.3261481
X-RAY DIFFRACTIONr_mcbond_other1.6232.3241480
X-RAY DIFFRACTIONr_mcangle_it2.3463.481851
X-RAY DIFFRACTIONr_mcangle_other2.3473.4821852
X-RAY DIFFRACTIONr_scbond_it3.1312.7431425
X-RAY DIFFRACTIONr_scbond_other3.132.7451426
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.823.9372080
X-RAY DIFFRACTIONr_long_range_B_refined5.84928.733371
X-RAY DIFFRACTIONr_long_range_B_other5.84828.7423372
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 144 -
Rwork0.274 2733 -
obs--99.97 %

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