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- PDB-8ufy: High Resolution structure of A. viridans Lactate Oxidase -

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Basic information

Entry
Database: PDB / ID: 8ufy
TitleHigh Resolution structure of A. viridans Lactate Oxidase
ComponentsL-lactate oxidase
KeywordsFLAVOPROTEIN / Biosensor / oxidase
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
FLAVIN MONONUCLEOTIDE / LACTIC ACID / PYRUVIC ACID / L-lactate oxidase
Similarity search - Component
Biological speciesAerococcus viridans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLodowski, D.T.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentNB18-20-24 United States
CitationJournal: Heliyon / Year: 2024
Title: An engineered lactate oxidase based electrochemical sensor for continuous detection of biomarker lactic acid in human sweat and serum.
Authors: He, Q. / Wang, C. / Jain, R. / Byrnes, J. / Farquhar, E.R. / Reed, E. / Berezovsky, E. / Chance, M.R. / Lodowski, D. / An, R.
History
DepositionOct 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)84,86810
Polymers83,4752
Non-polymers1,3938
Water6,702372
1
A: L-lactate oxidase
hetero molecules

A: L-lactate oxidase
hetero molecules

A: L-lactate oxidase
hetero molecules

A: L-lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,98524
Polymers166,9514
Non-polymers3,03420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area18550 Å2
ΔGint-40 kcal/mol
Surface area47120 Å2
MethodPISA
2
B: L-lactate oxidase
hetero molecules

B: L-lactate oxidase
hetero molecules

B: L-lactate oxidase
hetero molecules

B: L-lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,48916
Polymers166,9514
Non-polymers2,53812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area17920 Å2
ΔGint-72 kcal/mol
Surface area45230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.262, 132.262, 91.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-lactate oxidase


Mass: 41737.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus viridans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q44467

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Non-polymers , 5 types, 380 molecules

#2: 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PYR / PYRUVIC ACID


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


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 26-30.5% ETHYLENE GLYCOL, 100 mM MES ph 4.0, 125mM sodium Lactate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.17→75.35 Å / Num. obs: 517344 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 13.7 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.04 / Net I/σ(I): 9.7
Reflection shellResolution: 1.17→1.19 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 13078 / CC1/2: 0.349 / Rpim(I) all: 0.801 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5084refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→49.7 Å / SU ML: 0.1255 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.0314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1619 24194 5.05 %
Rwork0.1459 455005 -
obs0.1467 479199 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.83 Å2
Refinement stepCycle: LAST / Resolution: 1.2→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5435 0 94 372 5901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456215
X-RAY DIFFRACTIONf_angle_d0.80498512
X-RAY DIFFRACTIONf_chiral_restr0.0725883
X-RAY DIFFRACTIONf_plane_restr0.00711154
X-RAY DIFFRACTIONf_dihedral_angle_d13.23892308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.28988550.285815209X-RAY DIFFRACTION98.78
1.21-1.230.30267370.281715262X-RAY DIFFRACTION98.93
1.23-1.240.28778250.27615177X-RAY DIFFRACTION98.52
1.24-1.260.287870.263815135X-RAY DIFFRACTION98.43
1.26-1.280.27478290.256415076X-RAY DIFFRACTION98.31
1.28-1.290.26538640.25115084X-RAY DIFFRACTION98.33
1.29-1.310.27137250.247115198X-RAY DIFFRACTION98.22
1.31-1.330.24258100.24115129X-RAY DIFFRACTION98.22
1.33-1.350.25127890.21815075X-RAY DIFFRACTION98.01
1.35-1.370.23138140.208915115X-RAY DIFFRACTION98.08
1.37-1.40.227880.193515038X-RAY DIFFRACTION98
1.4-1.420.20228310.184915066X-RAY DIFFRACTION97.76
1.42-1.450.20617750.17414941X-RAY DIFFRACTION97.1
1.45-1.480.1858280.165914876X-RAY DIFFRACTION97.38
1.48-1.510.188740.145415224X-RAY DIFFRACTION99.11
1.51-1.550.16528350.131815297X-RAY DIFFRACTION99.94
1.55-1.590.14988310.125915350X-RAY DIFFRACTION99.94
1.59-1.630.15967750.12115449X-RAY DIFFRACTION99.89
1.63-1.680.14317770.110715382X-RAY DIFFRACTION99.73
1.68-1.730.12568460.10215244X-RAY DIFFRACTION99.64
1.73-1.790.12856990.105115513X-RAY DIFFRACTION99.72
1.79-1.860.14818180.111415289X-RAY DIFFRACTION99.69
1.86-1.950.14118420.112915305X-RAY DIFFRACTION99.59
1.95-2.050.14377700.118815307X-RAY DIFFRACTION99.46
2.05-2.180.14017780.117315299X-RAY DIFFRACTION98.98
2.18-2.350.149450.115614936X-RAY DIFFRACTION98.01
2.35-2.590.13187790.124414636X-RAY DIFFRACTION95.3
2.59-2.960.14087070.136414766X-RAY DIFFRACTION95.45
2.96-3.730.15398330.149715294X-RAY DIFFRACTION99.62
3.73-49.70.15628280.154215333X-RAY DIFFRACTION99.54

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