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- PDB-3d9f: Nitroalkane oxidase: active site mutant S276A crystallized with 1... -

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Basic information

Entry
Database: PDB / ID: 3d9f
TitleNitroalkane oxidase: active site mutant S276A crystallized with 1-nitrohexane
ComponentsNitroalkane oxidase
KeywordsOXIDOREDUCTASE / FLAVOENZYME / NITROALKANE / ACYL-COA DEHYDROGENASE / LONG CELL EDGE / FAD / INHIBITOR / FLAVOPROTEIN
Function / homology
Function and homology information


nitroalkane oxidase / nitroalkane oxidase activity / butyrate catabolic process / detoxification / oxidoreductase activity, acting on the CH-CH group of donors / fatty acid beta-oxidation using acyl-CoA dehydrogenase / FAD binding
Similarity search - Function
Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 ...Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 1-nitrohexane / Nitroalkane oxidase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHeroux, A. / Bozinovski, D.M. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M.
Citation
Journal: Biochemistry / Year: 2009
Title: Crystal structures of intermediates in the nitroalkane oxidase reaction.
Authors: Heroux, A. / Bozinovski, D.M. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M.
#1: Journal: Biochemistry / Year: 2006
Title: Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover.
Authors: Nagpal, A. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M.
#2: Journal: Biochemistry / Year: 2007
Title: Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase.
Authors: Fitzpatrick, P.F. / Bozinovski, D.M. / Heroux, A. / Shaw, P.G. / Valley, M.P. / Orville, A.M.
History
DepositionMay 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitroalkane oxidase
B: Nitroalkane oxidase
C: Nitroalkane oxidase
D: Nitroalkane oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,69220
Polymers192,2884
Non-polymers4,40416
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28210 Å2
ΔGint-148 kcal/mol
Surface area53250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.325, 108.325, 339.432
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Nitroalkane oxidase


Mass: 48072.051 Da / Num. of mol.: 4 / Mutation: S276A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Plasmid: PETNAO4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q8X1D8, nitroalkane oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-N6C / 1-nitrohexane


Mass: 131.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-30mM PEG 3350, 20-35% glycerol, 0.1M NaCacodylate, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 115243 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 43.94 Å2 / Rsym value: 0.069 / Net I/σ(I): 26.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1 / Num. unique all: 9698 / Rsym value: 0.552 / % possible all: 83.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.781 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24097 5789 5 %RANDOM
Rwork0.20008 ---
all0.20216 118169 --
obs0.20216 109423 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.946 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20.62 Å20 Å2
2--1.24 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13210 0 296 468 13974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213790
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.98918734
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76951718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26924.453548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.493152316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3841572
X-RAY DIFFRACTIONr_chiral_restr0.0930.22122
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210196
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.26946
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.29407
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2750
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4170.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6641.58863
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.066213818
X-RAY DIFFRACTIONr_scbond_it1.73135669
X-RAY DIFFRACTIONr_scangle_it2.6394.54916
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 320 -
Rwork0.27 6544 -
obs--79.11 %

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