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- PDB-2c0u: Crystal Structure of a Covalent Complex of Nitroalkane Oxidase Tr... -

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Basic information

Entry
Database: PDB / ID: 2c0u
TitleCrystal Structure of a Covalent Complex of Nitroalkane Oxidase Trapped During Substrate Turnover
ComponentsNITROALKANE OXIDASE
KeywordsOXIDOREDUCTASE / N5-FAD ADDUCT / FLAVOENZYME / NITROALKANE / ACYL-COA DEHYDROGENASE / NITROBUTYL / FAD / 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
FLAVIN-ADENINE DINUCLEOTIDE / (2S)-2-NITROBUTANE / Nitroalkane oxidase
Similarity search - Component
Biological speciesFUSARIUM OXYSPORUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 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.
History
DepositionSep 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,05812
Polymers195,5034
Non-polymers3,5558
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.390, 163.739, 173.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NITROALKANE OXIDASE


Mass: 48875.773 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
#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-NBT / (2S)-2-NITROBUTANE


Mass: 103.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growpH: 7.5
Details: 20%(W/V) PEG 1500, 300MM AMMONIUM SULPHATE, 150 MM PIPES PH 7.5, 10 MM TCEP-HCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9794, 0.9611, 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 19, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.96111
30.97951
ReflectionResolution: 2.2→40 Å / Num. obs: 130755 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 11.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE N5-(2-NITROBUTYL)-1,5- DIHYDRO- FAD COVALENT INTERMEDIATE WAS TRAPPED DURING TURNOVER OF NEUTRAL NITROETHANE IN THE PRESENCE OF NITROETHANE ANION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 6519 5 %RANDOM
Rwork0.2014 ---
obs0.2014 130649 99.8 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 44.8263 Å2 / ksol: 0.348862 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13228 0 240 692 14160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006528
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.08887
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MSE_XPLOR.PARAMMSE_XPLOR.TOP
X-RAY DIFFRACTION5DRGCNS_TRANS.PARAMDRGCNS_TRANS.TOP

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