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- PDB-2zfa: Structure of Lactate Oxidase at pH4.5 from AEROCOCCUS VIRIDANS -

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Basic information

Entry
Database: PDB / ID: 2zfa
TitleStructure of Lactate Oxidase at pH4.5 from AEROCOCCUS VIRIDANS
ComponentsLactate oxidase
KeywordsOXIDOREDUCTASE / L-LACTATE OXIDASE / FLAVOENZYME / FMN / D-LACTATE / Flavoprotein
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 / L-lactate oxidase
Similarity search - Component
Biological speciesAerococcus viridans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsFuruichi, M. / Balasundaresan, D. / Suzuki, N. / Yoshida, Y. / Minagawa, H. / 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
DepositionDec 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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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)82,9996
Polymers81,9622
Non-polymers1,0374
Water7,116395
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)331,99424
Polymers327,8478
Non-polymers4,14716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
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)165,99712
Polymers163,9234
Non-polymers2,0748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area17350 Å2
ΔGint-49.1 kcal/mol
Surface area46950 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)165,99712
Polymers163,9234
Non-polymers2,0748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area15800 Å2
ΔGint-41.2 kcal/mol
Surface area45410 Å2
Unit cell
Length a, b, c (Å)132.595, 132.595, 90.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-491-

HOH

21B-499-

HOH

31B-500-

HOH

41B-504-

HOH

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Components

#1: Protein Lactate oxidase


Mass: 40980.852 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 40% Ethylene Glycol, 100mM acetate buffer (pH 4.5), VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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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 210 / Detector: CCD / Date: Apr 23, 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: 1.81→50 Å / Num. all: 71662 / Num. obs: 71313 / % possible obs: 99.5 % / Redundancy: 14.8 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 61.3
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 6.9 / Num. unique all: 6967 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOX

1gox


Resolution: 1.81→34.09 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.304 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20757 3612 5.1 %RANDOM
Rwork0.18437 ---
obs0.18557 67698 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.679 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.81→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5228 0 70 395 5693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225415
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9657347
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34324.211247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10915856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0231532
X-RAY DIFFRACTIONr_chiral_restr0.1020.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024163
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22706
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23797
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2378
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.2143
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0251.53442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60625370
X-RAY DIFFRACTIONr_scbond_it2.5332311
X-RAY DIFFRACTIONr_scangle_it3.9344.51977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.811→1.858 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 268 -
Rwork0.224 4998 -
obs--99.6 %

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