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- PDB-3d9g: Nitroalkane oxidase: wild type crystallized in a trapped state fo... -

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Basic information

Entry
Database: PDB / ID: 3d9g
TitleNitroalkane oxidase: wild type crystallized in a trapped state forming a cyanoadduct with FAD
ComponentsNitroalkane oxidase
KeywordsOXIDOREDUCTASE / FLAVOENZYME / NITROALKANE / ACYL-COA DEHYDROGENASE / LONG CELL EDGE / FAD / INHIBITOR / FLAVOPROTEIN
Function / homology
Function and homology information


nitroalkane oxidase activity / nitroalkane oxidase / : / butyrate catabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / : / oxidoreductase activity, acting on the CH-CH group of donors / FAD binding
Similarity search - Function
Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily ...Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / 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
heptanenitrile / FLAVIN-ADENINE DINUCLEOTIDE / Nitroalkane oxidase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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)196,12314
Polymers192,3524
Non-polymers3,77110
Water15,133840
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26480 Å2
ΔGint-151 kcal/mol
Surface area53950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.256, 109.256, 343.945
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: 48088.051 Da / Num. of mol.: 4
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-CNX / heptanenitrile / 1-cyanohexane


Mass: 111.185 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
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: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2007 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 122023 / % possible obs: 94.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 27.4
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 1.9 / Num. unique all: 8294 / Rsym value: 0.304 / % possible all: 64.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C12

2c12


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.821 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.233 6137 5 %RANDOM
Rwork0.194 ---
all0.196 129624 --
obs0.196 115721 94 %-
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: 38.046 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.52 Å20 Å2
2--1.05 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13233 0 256 840 14329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213810
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.99118779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27151723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2824.348552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.925152341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1561576
X-RAY DIFFRACTIONr_chiral_restr0.090.22128
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210240
X-RAY DIFFRACTIONr_nbd_refined0.2010.26869
X-RAY DIFFRACTIONr_nbtor_refined0.30.29465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2910
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.210
X-RAY DIFFRACTIONr_mcbond_it0.6191.58891
X-RAY DIFFRACTIONr_mcangle_it0.982213855
X-RAY DIFFRACTIONr_scbond_it1.63435685
X-RAY DIFFRACTIONr_scangle_it2.5344.54924
LS refinement shellResolution: 2.154→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 293 -
Rwork0.243 5393 -
all-5686 -
obs--60.41 %

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