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- PDB-5lsm: Crystal structure of nitronate monooxygenase (SO_0471) from Shewa... -

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Basic information

Entry
Database: PDB / ID: 5lsm
TitleCrystal structure of nitronate monooxygenase (SO_0471) from Shewanella oneidensis MR-1
ComponentsFMN-dependent nitronate monooxygenase
KeywordsOXIDOREDUCTASE / NITRONATE MONOXYGENASE / 2-NITROPROPANE
Function / homology
Function and homology information


nitronate monooxygenase activity / response to toxic substance / nucleotide binding
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Propionate 3-nitronate monooxygenase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBaker, G.E. / Race, P.R.
CitationJournal: To Be Published
Title: Crystal structure of nitronate monooxygenase (SO_0471) from Shewanella oneidensis MR-1
Authors: Baker, G.E. / Race, P.R.
History
DepositionSep 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: FMN-dependent nitronate monooxygenase
B: FMN-dependent nitronate monooxygenase
C: FMN-dependent nitronate monooxygenase
D: FMN-dependent nitronate monooxygenase
E: FMN-dependent nitronate monooxygenase
F: FMN-dependent nitronate monooxygenase
G: FMN-dependent nitronate monooxygenase
H: FMN-dependent nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,17420
Polymers304,1558
Non-polymers4,01912
Water7,638424
1
H: FMN-dependent nitronate monooxygenase
hetero molecules

A: FMN-dependent nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0435
Polymers76,0392
Non-polymers1,0053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
2
G: FMN-dependent nitronate monooxygenase
hetero molecules

E: FMN-dependent nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1366
Polymers76,0392
Non-polymers1,0974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
3
A: FMN-dependent nitronate monooxygenase
hetero molecules

H: FMN-dependent nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0435
Polymers76,0392
Non-polymers1,0053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4600 Å2
ΔGint-25 kcal/mol
Surface area24250 Å2
MethodPISA
4
B: FMN-dependent nitronate monooxygenase
C: FMN-dependent nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9514
Polymers76,0392
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-25 kcal/mol
Surface area23860 Å2
MethodPISA
5
D: FMN-dependent nitronate monooxygenase
F: FMN-dependent nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0435
Polymers76,0392
Non-polymers1,0053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-27 kcal/mol
Surface area24260 Å2
MethodPISA
6
E: FMN-dependent nitronate monooxygenase
hetero molecules

G: FMN-dependent nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1366
Polymers76,0392
Non-polymers1,0974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area4820 Å2
ΔGint-29 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.001, 99.911, 108.558
Angle α, β, γ (deg.)95.31, 106.23, 91.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
FMN-dependent nitronate monooxygenase


Mass: 38019.324 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: SO_0471 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EJJ2, nitronate monooxygenase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 M potassium dihydrogen phosphate and 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97833 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97833 Å / Relative weight: 1
ReflectionResolution: 2.5→34.16 Å / Num. obs: 99971 / % possible obs: 95 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.343 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GJL

2gjl


Resolution: 2.5→34.16 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.444 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.554 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25572 5038 5 %RANDOM
Rwork0.18516 ---
obs0.18866 94928 94.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.158 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å2-0.29 Å2-0.79 Å2
2--0.39 Å2-0.24 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19289 0 272 424 19985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01919983
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218597
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.96927285
X-RAY DIFFRACTIONr_angle_other_deg0.7342517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.87252650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.31323.913713
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.064152757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4281593
X-RAY DIFFRACTIONr_chiral_restr0.0960.23189
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02122903
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024434
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_it3.8984.31910693
X-RAY DIFFRACTIONr_mcbond_other3.8984.31910692
X-RAY DIFFRACTIONr_mcangle_it5.4976.46913312
X-RAY DIFFRACTIONr_mcangle_other5.4976.46913313
X-RAY DIFFRACTIONr_scbond_it4.274.6019290
X-RAY DIFFRACTIONr_scbond_other4.274.6019290
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1666.78513974
X-RAY DIFFRACTIONr_long_range_B_refined7.936.51422664
X-RAY DIFFRACTIONr_long_range_B_other7.936.51522665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 381 -
Rwork0.283 7053 -
obs--95.52 %

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