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- PDB-2zaf: Mechanistic and Structural Analyses of the Roles of Arg409 and As... -

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Basic information

Entry
Database: PDB / ID: 2zaf
TitleMechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase
ComponentsNitroalkane oxidase
KeywordsOXIDOREDUCTASE / FLAVOENZYME / NITROALKANE / 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 / Nitroalkane oxidase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsFitzpatrick, P.F. / Bozinovski, D.M. / Heroux, A. / Shaw, P.G. / Valley, M.P. / Orville, A.M.
Citation
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.
#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.
History
DepositionOct 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)195,9078
Polymers192,7654
Non-polymers3,1424
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26120 Å2
ΔGint-157 kcal/mol
Surface area54580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.319, 108.319, 340.012
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 2 - 431 / Label seq-ID: 2 - 431

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Nitroalkane oxidase


Mass: 48191.230 Da / Num. of mol.: 4 / Mutation: R409K
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

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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: 58.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25-30%(W/V) PEG 3350, 35% (V/V) GLYCEROL, 200MM SODIUM CACODYLATE TRIHYDRATE, pH 7.5, 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: Aug 15, 2006 / Details: mirrors
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: 2.5→50 Å / Num. all: 81166 / Num. obs: 81166 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.128 / Net I/σ(I): 17.1
Reflection shellResolution: 2.5→2.74 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.587 / % possible all: 93.2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementStarting model: 1c0u

1c0u


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.543 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3776 5.1 %RANDOM
Rwork0.228 ---
obs0.23 73886 91.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.31 Å20 Å2
2--0.63 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13228 0 212 0 13440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213736
X-RAY DIFFRACTIONr_angle_refined_deg1.321.98618676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.38151716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90924.453548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.424152344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9121572
X-RAY DIFFRACTIONr_chiral_restr0.0880.22120
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210168
X-RAY DIFFRACTIONr_nbd_refined0.2220.26574
X-RAY DIFFRACTIONr_nbtor_refined0.3070.29395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2425
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.22
X-RAY DIFFRACTIONr_mcbond_it0.4241.58572
X-RAY DIFFRACTIONr_mcangle_it0.802213812
X-RAY DIFFRACTIONr_scbond_it1.22135164
X-RAY DIFFRACTIONr_scangle_it2.0124.54864
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1720MEDIUM POSITIONAL0.160.5
2B1720MEDIUM POSITIONAL0.140.5
3C1720MEDIUM POSITIONAL0.150.5
4D1720MEDIUM POSITIONAL0.150.5
1A1587LOOSE POSITIONAL0.285
2B1587LOOSE POSITIONAL0.275
3C1587LOOSE POSITIONAL0.35
4D1587LOOSE POSITIONAL0.325
1A1720MEDIUM THERMAL0.722
2B1720MEDIUM THERMAL0.82
3C1720MEDIUM THERMAL0.592
4D1720MEDIUM THERMAL0.822
1A1587LOOSE THERMAL1.4910
2B1587LOOSE THERMAL1.7210
3C1587LOOSE THERMAL1.4310
4D1587LOOSE THERMAL1.7110
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 220 -
Rwork0.351 3961 -
all-4181 -
obs--70.49 %

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