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- PDB-3d9d: Nitroalkane oxidase: mutant D402N crystallized with 1-nitrohexane -

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Basic information

Entry
Database: PDB / ID: 3d9d
TitleNitroalkane oxidase: mutant D402N crystallized with 1-nitrohexane
ComponentsNitroalkane oxidase
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE 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 / MOLREP / Resolution: 2.1 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 1.3Nov 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 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)196,75220
Polymers192,3484
Non-polymers4,40416
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28150 Å2
ΔGint-146 kcal/mol
Surface area53630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.875, 107.875, 338.442
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Nitroalkane oxidase


Mass: 48087.066 Da / Num. of mol.: 4 / Mutation: D402N
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.: 650 / 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: 2.96 Å3/Da / Density % sol: 58.38 %
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: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 9, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 391270 / Num. obs: 391270 / % possible obs: 91.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 13.72
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 1.2 / Num. unique all: 8209 / Rsym value: 0.447 / % possible all: 62.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLREP
Starting model: 2c12

2c12


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.337 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.192 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.219 6169 5 %RANDOM
Rwork0.18 ---
all0.182 133933 --
obs0.182 123030 91.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.174 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13219 0 296 650 14165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213799
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.98818747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45451720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10124.453548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.079152315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.291572
X-RAY DIFFRACTIONr_chiral_restr0.1380.22124
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210204
X-RAY DIFFRACTIONr_nbd_refined0.2090.26959
X-RAY DIFFRACTIONr_nbtor_refined0.3040.29475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2834
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4280.27
X-RAY DIFFRACTIONr_mcbond_it1.1581.58875
X-RAY DIFFRACTIONr_mcangle_it1.292213834
X-RAY DIFFRACTIONr_scbond_it2.36235660
X-RAY DIFFRACTIONr_scangle_it3.6354.54913
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 273 -
Rwork0.267 5419 -
all-5692 -
obs--58.18 %

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