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- PDB-2nli: Crystal Structure of the complex between L-lactate oxidase and a ... -

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Basic information

Entry
Database: PDB / ID: 2nli
TitleCrystal Structure of the complex between L-lactate oxidase and a substrate analogue at 1.59 angstrom resolution
ComponentsLactate oxidase
KeywordsOXIDOREDUCTASE / L-lactate oxidase / flavoenzyme / FMN / D-Lactate
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 class I / Aldolase-type TIM barrel ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / LACTIC ACID / HYDROGEN PEROXIDE / L-lactate oxidase
Similarity search - Component
Biological speciesAerococcus viridans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsFuruichi, M. / Suzuki, N. / Balasundaresan, D. / Yoshida, Y. / Minagawa, H. / Watanabe, Y. / Kaneko, H. / Waga, I. / Kumar, P.K.R. / Mizuno, H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: X-ray structures of Aerococcus viridans lactate oxidase and its complex with D-lactate at pH 4.5 show an alpha-hydroxyacid oxidation mechanism
Authors: Furuichi, M. / Suzuki, N. / Dhakshnamoorhty, B. / Minagawa, H. / Yamagishi, R. / Watanabe, Y. / Goto, Y. / Kaneko, H. / Yoshida, Y. / Yagi, H. / Waga, I. / Kumar, P.K.R. / Mizuno, H.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactate oxidase
B: Lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7198
Polymers80,5582
Non-polymers1,1616
Water11,187621
1
A: Lactate oxidase
B: Lactate oxidase
hetero molecules

A: Lactate oxidase
B: Lactate oxidase
hetero molecules

A: Lactate oxidase
B: Lactate oxidase
hetero molecules

A: Lactate oxidase
B: Lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,87632
Polymers322,2338
Non-polymers4,64324
Water1448
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
MethodPQS
2
A: Lactate oxidase
hetero molecules

A: Lactate oxidase
hetero molecules

A: Lactate oxidase
hetero molecules

A: Lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,43816
Polymers161,1164
Non-polymers2,32212
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 area16510 Å2
ΔGint-58 kcal/mol
Surface area47020 Å2
MethodPISA
3
B: Lactate oxidase
hetero molecules

B: Lactate oxidase
hetero molecules

B: Lactate oxidase
hetero molecules

B: Lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,43816
Polymers161,1164
Non-polymers2,32212
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 area15580 Å2
ΔGint-67 kcal/mol
Surface area44710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.422, 132.422, 90.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Lactate oxidase


Mass: 40279.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus viridans (bacteria) / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q44467, lactate 2-monooxygenase
#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-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND, LAC, REPRESENTS D-LACTIC ACID. THE CHEMICAL COMPONENT DICTIONARY WILL BE RENAMED TO BE ...THE LIGAND, LAC, REPRESENTS D-LACTIC ACID. THE CHEMICAL COMPONENT DICTIONARY WILL BE RENAMED TO BE CONSIST WITH THE CORRECT FORM SHORTLY.

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2005
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. all: 103948 / Num. obs: 103948 / % possible obs: 98.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 5.8 % / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOX

1gox


Resolution: 1.59→41.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.488 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 5190 5 %RANDOM
Rwork0.177 ---
obs0.178 98757 99 %-
all-103948 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.59 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.59→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5213 0 78 621 5912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225413
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9677341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1445672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46124.194248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51715857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5621532
X-RAY DIFFRACTIONr_chiral_restr0.0860.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024167
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22813
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23798
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2570
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.2162
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8431.53422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32425345
X-RAY DIFFRACTIONr_scbond_it2.13532333
X-RAY DIFFRACTIONr_scangle_it3.3614.51996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 321 -
Rwork0.292 6615 -
obs--89.68 %

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