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- PDB-6m74: Crystal structure of Enterococcus hirae L-lactate oxidase M207L i... -

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Basic information

Entry
Database: PDB / ID: 6m74
TitleCrystal structure of Enterococcus hirae L-lactate oxidase M207L in complex with D-lactate form ligand
ComponentsL-lactate oxidase
KeywordsOXIDOREDUCTASE / L-lactate oxidase / FMN / Enterococcus hirae / L-lactate
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-type TIM barrel
Similarity search - Domain/homology
Chem-FNR / LACTIC ACID / TRIETHYLENE GLYCOL / PYRUVIC ACID / L-lactate oxidase
Similarity search - Component
Biological speciesEnterococcus hirae ATCC 9790 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsYoshida, H. / Hiraka, K. / Tsugawa, W. / Sode, K.
CitationJournal: Protein Sci. / Year: 2022
Title: Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper
Authors: Hiraka, K. / Yoshida, H. / Tsugawa, W. / Asano, R. / La Belle, J.T. / Ikebukuro, K. / Sode, K.
History
DepositionMar 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.ptnr2_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1349
Polymers40,0391
Non-polymers1,0958
Water5,026279
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)164,53636
Polymers160,1564
Non-polymers4,38032
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 area22330 Å2
ΔGint-10 kcal/mol
Surface area47200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.130, 138.130, 127.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein L-lactate oxidase


Mass: 40039.027 Da / Num. of mol.: 1 / Mutation: M207L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus hirae ATCC 9790 (bacteria)
Gene: EHR_08130, I584_00297 / Plasmid: pET30c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6SYK8, (S)-2-hydroxy-acid oxidase

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Non-polymers , 7 types, 287 molecules

#2: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P
#3: Chemical ChemComp-LAC / LACTIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris, PEG MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→19.54 Å / Num. obs: 93906 / % possible obs: 99.9 % / Redundancy: 13.104 % / Biso Wilson estimate: 23.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.063 / Χ2: 0.965 / Net I/σ(I): 26.96 / Num. measured all: 1230530 / Scaling rejects: 183
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.52-1.5613.0780.7034.3689913688268750.9420.73199.9
1.56-1.612.5060.5345.4283855671067050.9530.55799.9
1.6-1.6513.5180.4077.4788203652765250.9740.423100
1.65-1.713.5270.3279.2585340631063090.9830.34100
1.7-1.7613.4320.24911.6182766616361620.9890.259100
1.76-1.8213.360.19813.9379601595859580.9930.206100
1.82-1.8913.1620.15217.4275684575057500.9960.158100
1.89-1.9612.8190.11921.2971016554055400.9970.124100
1.96-2.0511.9980.09324.863697530953090.9970.098100
2.05-2.1513.0580.07531.6466454508950890.9980.078100
2.15-2.2712.4610.06336.0160562486048600.9980.066100
2.27-2.413.8720.05941.0563714459345930.9990.061100
2.4-2.5713.8530.05544.7759941432743270.9990.057100
2.57-2.7813.6260.04948.8955377406440640.9990.051100
2.78-3.0413.2730.04551.8149311371537150.9990.047100
3.04-3.412.7030.04155.443064339033900.9990.043100
3.4-3.9212.1980.03660.2736826301930190.9990.037100
3.92-4.8112.6880.03364.2632444255725570.9990.035100
4.81-6.813.9430.03566.8928305203020300.9990.036100
6.8-19.5412.8050.03466.5214457119111290.9990.03594.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M73

6m73


Resolution: 1.52→19.54 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.301 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1444 4714 5 %RANDOM
Rwork0.1279 ---
obs0.1287 89192 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.96 Å2 / Biso mean: 16.448 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0 Å2
2---0.54 Å20 Å2
3---1.09 Å2
Refinement stepCycle: final / Resolution: 1.52→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 73 279 3135
Biso mean--22.83 28.17 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132953
X-RAY DIFFRACTIONr_bond_other_d00.0172702
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.6484000
X-RAY DIFFRACTIONr_angle_other_deg1.4571.5836274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0475375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80922.848151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77515475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1721516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023344
X-RAY DIFFRACTIONr_gen_planes_other00.02612
X-RAY DIFFRACTIONr_rigid_bond_restr5.56335655
LS refinement shellResolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 345 -
Rwork0.201 6527 -
all-6872 -
obs--99.87 %

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