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- PDB-2c12: Crystal Structure of Nitroalkane Oxidase in Complex with Spermine... -

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Basic information

Entry
Database: PDB / ID: 2c12
TitleCrystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor
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 / SPERMINE / Nitroalkane oxidase
Similarity search - Component
Biological speciesFUSARIUM OXYSPORUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsNagpal, A. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and Preliminary Analysis of Active Nitroalkane Oxidase in Three Crystal Forms
Authors: Nagpal, A. / Valley, M.P. / Fitzpatrick, P.F. / Orville, A.M.
#2: Journal: Arch.Biochem.Biophys. / Year: 2005
Title: Nitroalkane Oxidase, a Carbanion-Forming Flavoprotein Homologous to Acyl-Coa Dehydrogenase
Authors: Fitzpatrick, P.F. / Orville, A.M. / Nagpal, A. / Valley, M.P.
History
DepositionSep 10, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
E: NITROALKANE OXIDASE
F: NITROALKANE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,92833
Polymers289,3156
Non-polymers7,61327
Water20,1231117
1
A: NITROALKANE OXIDASE
B: NITROALKANE OXIDASE
C: NITROALKANE OXIDASE
D: NITROALKANE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,99423
Polymers192,8774
Non-polymers5,11719
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31330 Å2
ΔGint-143.8 kcal/mol
Surface area52880 Å2
MethodPISA
2
E: NITROALKANE OXIDASE
F: NITROALKANE OXIDASE
hetero molecules

E: NITROALKANE OXIDASE
F: NITROALKANE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,86920
Polymers192,8774
Non-polymers4,99316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area30490 Å2
ΔGint-138.5 kcal/mol
Surface area52960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.393, 103.393, 485.134
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
NITROALKANE OXIDASE


Mass: 48219.246 Da / Num. of mol.: 6
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

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Non-polymers , 5 types, 1144 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H26N4
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1117 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.2 %
Crystal growpH: 7.5
Details: 25%(W/V) PEG 4000, 35% (V/V) GLYCEROL, 200 MM SODIUM CACODYLATE TRIHYDRATE PH 7.5, 1 MM SPERMINE TETRAHYDROCHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 180533 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 1.64 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.6
Reflection shellResolution: 2.07→2.15 Å / Redundancy: 1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3 / % possible all: 81.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C0U

2c0u


Resolution: 2.07→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.182 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 9048 5 %RANDOM
Rwork0.188 ---
obs0.19 171484 97.8 %-
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: 24.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19842 0 512 1117 21471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02220793
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218829
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.98728204
X-RAY DIFFRACTIONr_angle_other_deg0.992343945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42252574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.23192
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222636
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023870
X-RAY DIFFRACTIONr_nbd_refined0.2150.24879
X-RAY DIFFRACTIONr_nbd_other0.2440.223597
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.211803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.21228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.2172
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5751.512858
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11220720
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.87437935
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.134.57484
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.12 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 495
Rwork0.226 9710

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