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- PDB-4qis: Crystal structure of Nitroalkane Oxidase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4qis
TitleCrystal structure of Nitroalkane Oxidase from Pseudomonas aeruginosa
ComponentsNitronate monooxygenase family protein
KeywordsOXIDOREDUCTASE / TIM barrel / FMN Binding / cytosol
Function / homology
Function and homology information


nitroalkane oxidase activity / nitronate monooxygenase activity / response to toxic substance / nucleotide binding
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Propionate 3-nitronate monooxygenase / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.906 Å
AuthorsChi, Y.M. / Lee, J.H.
CitationJournal: To be Published
Title: Crystal structures and reaction mechanisms of nitroalkane oxidase (NAO) from Pseudomonas aeruginosa
Authors: Chi, Y.M. / Lee, J.H.
History
DepositionJun 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitronate monooxygenase family protein
B: Nitronate monooxygenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9514
Polymers75,0382
Non-polymers9132
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-21 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.895, 54.834, 88.202
Angle α, β, γ (deg.)90.00, 95.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nitronate monooxygenase family protein / NAO / nitroalkane oxidase


Mass: 37518.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO581 / Gene: M801_4200 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: T2E9U5, UniProt: A0A0M3KKW0*PLUS, nitroalkane oxidase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.2M Ammonium fluoride, 20% polyethylene glycol 3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 22, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38.921 Å / Num. all: 52206 / Num. obs: 50640 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.34 Å2
Reflection shellResolution: 1.9→1.93 Å / % possible all: 82.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BW2

3bw2


Resolution: 1.906→38.921 Å / FOM work R set: 0.8294 / SU ML: 0.26 / σ(F): 0.31 / Phase error: 24.7 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2000 3.95 %random
Rwork0.1906 ---
all0.1929 52206 --
obs0.1929 50640 97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.4 Å2 / Biso mean: 21.14 Å2 / Biso min: 4.81 Å2
Refinement stepCycle: LAST / Resolution: 1.906→38.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5128 0 62 721 5911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085298
X-RAY DIFFRACTIONf_angle_d1.1297221
X-RAY DIFFRACTIONf_chiral_restr0.069818
X-RAY DIFFRACTIONf_plane_restr0.005957
X-RAY DIFFRACTIONf_dihedral_angle_d14.5921931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9057-1.95330.34031240.26973020314485
1.9533-2.00610.30991350.25793266340192
2.0061-2.06520.32481380.23813370350894
2.0652-2.13180.31531410.21663429357096
2.1318-2.2080.27281420.20833457359997
2.208-2.29640.28331420.19953453359598
2.2964-2.40090.25111450.20013528367398
2.4009-2.52750.25121460.20133528367499
2.5275-2.68580.28661450.20353553369899
2.6858-2.89310.2571470.2023568371599
2.8931-3.18410.2331470.198735663713100
3.1841-3.64460.23511470.175335943741100
3.6446-4.59060.19851480.157336113759100
4.5906-38.92890.21081530.154736973850100

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