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- PDB-4qiu: Crystal structure of Nitroalkane Oxidase from Pseudomonas aerugin... -

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Basic information

Entry
Database: PDB / ID: 4qiu
TitleCrystal structure of Nitroalkane Oxidase from Pseudomonas aeruginosa in Mutant complex form
ComponentsNitronate monooxygenase family protein
KeywordsOXIDOREDUCTASE / TIM barrel / FMN / 1NP
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 / 1-nitropropane / Propionate 3-nitronate monooxygenase / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 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)76,0596
Polymers74,9682
Non-polymers1,0914
Water14,322795
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-19 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.066, 56.794, 87.237
Angle α, β, γ (deg.)90.00, 97.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37483.965 Da / Num. of mol.: 2 / Mutation: H183C
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: A0A0M3KKW2*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: Chemical ChemComp-N1P / 1-nitropropane


Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% P550MME_P20K, pH 7.5, 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 5, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→34.765 Å / Num. all: 133657 / Num. obs: 130396 / % possible obs: 97.56 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.76 Å2
Reflection shellResolution: 1.4→1.45 Å / % possible all: 90.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BW2

3bw2


Resolution: 1.401→34.765 Å / FOM work R set: 0.8704 / SU ML: 0.16 / σ(F): 1.48 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 1939 1.49 %random
Rwork0.1753 ---
all0.1756 130396 --
obs0.1756 130396 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.98 Å2 / Biso mean: 18.72 Å2 / Biso min: 6.78 Å2
Refinement stepCycle: LAST / Resolution: 1.401→34.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 74 795 6023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065332
X-RAY DIFFRACTIONf_angle_d1.0467262
X-RAY DIFFRACTIONf_chiral_restr0.04822
X-RAY DIFFRACTIONf_plane_restr0.005962
X-RAY DIFFRACTIONf_dihedral_angle_d12.261948
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 (%)
1.4008-1.43580.36751230.32438477860091
1.4358-1.47470.29161280.29428873900194
1.4747-1.51810.29831360.2678940907696
1.5181-1.56710.26421350.23919027916296
1.5671-1.62310.25541410.22239091923297
1.6231-1.6880.23481360.20179070920697
1.688-1.76490.27161370.18519194933198
1.7649-1.85790.20431430.17539258940199
1.8579-1.97430.17361420.15929277941999
1.9743-2.12670.18711420.15549375951799
2.1267-2.34070.18121430.153693769519100
2.3407-2.67930.18321420.163194249566100
2.6793-3.37520.18851440.167294689612100
3.3752-34.77580.16231470.149796079754100

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