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- PDB-6rhs: Crystal structure of Pediococcus acidilactici (Putative)lactate o... -

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Basic information

Entry
Database: PDB / ID: 6rhs
TitleCrystal structure of Pediococcus acidilactici (Putative)lactate oxidase Refolded WT protein
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: 2.6 Å
AuthorsAshok, Y. / Maksimainen, M.M. / Kilpelainen, P. / 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 22, 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 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Putative L-lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3594
Polymers39,7191
Non-polymers6413
Water36020
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)161,43716
Polymers158,8754
Non-polymers2,56212
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 area16830 Å2
ΔGint-68 kcal/mol
Surface area47820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.500, 135.500, 125.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Putative L-lactate oxidase


Mass: 39718.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MTMINGYEQSDREEKIDILNLESLEKQAEEIIPAGGFGYIAGGSEDEWTLKQNRMAFHHR QIAPKALSGIEKPELNTEIFGIPLNTPVMMAPAAAQGLAHSQGEKDTARGLAAVGGLMAQ STYSSVSIAETAAAGGDAPQFFQLYMSKDWNFNESLLDEAKKANVKAIILTVDATVDGYR ...Details: MTMINGYEQSDREEKIDILNLESLEKQAEEIIPAGGFGYIAGGSEDEWTLKQNRMAFHHR QIAPKALSGIEKPELNTEIFGIPLNTPVMMAPAAAQGLAHSQGEKDTARGLAAVGGLMAQ STYSSVSIAETAAAGGDAPQFFQLYMSKDWNFNESLLDEAKKANVKAIILTVDATVDGYR EADIKNKFTFPLPMANLIKFSEGNGQGKGIEEIYASAAQNIRPEDVKRIADYTNLPVIVK GIQTPEDAIRAIDAGAAGIYVSNHGGRQLNGGPASFDVLEDIATAVNKQVPIIFDSGVRR GSDVFKALASGADLVALGRPVIYGLALGGAKGVQSVFEHLNHELEIVMQLAGTKTIEDVK NNSLLNIKY
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging 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: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 18301 / % possible obs: 100 % / Redundancy: 13.3 % / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.67 Å / Num. unique obs: 1328

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R9V

6r9v


Resolution: 2.6→47.95 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.366 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.228 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21514 868 4.7 %RANDOM
Rwork0.18585 ---
obs0.18728 17433 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.766 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-0 Å2
2---1.45 Å20 Å2
3---2.9 Å2
Refinement stepCycle: 1 / Resolution: 2.6→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 43 20 2770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132835
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172632
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6513845
X-RAY DIFFRACTIONr_angle_other_deg1.3031.5826114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.025364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23424.074135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13115462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4171512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023207
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02543
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_it2.5213.7691456
X-RAY DIFFRACTIONr_mcbond_other2.5223.7671455
X-RAY DIFFRACTIONr_mcangle_it3.665.6511817
X-RAY DIFFRACTIONr_mcangle_other3.6595.6531818
X-RAY DIFFRACTIONr_scbond_it3.6414.1651379
X-RAY DIFFRACTIONr_scbond_other3.6424.1671380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5836.0892028
X-RAY DIFFRACTIONr_long_range_B_refined6.84544.3343148
X-RAY DIFFRACTIONr_long_range_B_other6.84544.3473149
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 62 -
Rwork0.292 1264 -
obs--100 %

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