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

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Basic information

Entry
Database: PDB / ID: 4qit
TitleCrystal structure of Nitroalkane Oxidase from Pseudomonas aeruginosa in mutant complex form
ComponentsNitronate monooxygenase family protein
KeywordsOXIDOREDUCTASE / TIM barrel / FMN / NIE
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 / nitroethane / Propionate 3-nitronate monooxygenase / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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)76,2616
Polymers75,1982
Non-polymers1,0634
Water15,835879
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-18 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.189, 56.851, 87.307
Angle α, β, γ (deg.)90.00, 97.08, 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: 37599.094 Da / Num. of mol.: 2 / Mutation: H183S
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: A0A0M3KKW1*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-NIE / nitroethane


Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 879 / 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: 46.49 %
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→34.907 Å / Num. all: 134387 / Num. obs: 132614 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 12.63 Å2
Reflection shellResolution: 1.4→1.45 Å / % possible all: 96.2

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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: 1.4→34.907 Å / FOM work R set: 0.8872 / SU ML: 0.16 / σ(F): 1.49 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 6622 4.99 %
Rwork0.1755 --
all0.1767 132614 -
obs0.1767 132614 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.32 Å2 / Biso mean: 17.81 Å2 / Biso min: 5.69 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 72 879 6105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065330
X-RAY DIFFRACTIONf_angle_d1.1147260
X-RAY DIFFRACTIONf_chiral_restr0.07823
X-RAY DIFFRACTIONf_plane_restr0.005961
X-RAY DIFFRACTIONf_dihedral_angle_d12.5431948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.32992110.3144056426796
1.4159-1.43260.36392170.29814107432496
1.4326-1.450.31422110.29144046425797
1.45-1.46840.27732110.2714125433697
1.4684-1.48770.30732170.25574112432997
1.4877-1.50810.24582190.25054111433097
1.5081-1.52960.24762210.2364176439798
1.5296-1.55250.26082150.22164127434298
1.5525-1.57670.25992220.22154138436098
1.5767-1.60260.23962170.21164148436598
1.6026-1.63020.24742210.20634190441198
1.6302-1.65990.22212150.19714172438799
1.6599-1.69180.22022200.19384180440099
1.6918-1.72630.20372200.18154199441999
1.7263-1.76390.21772180.17174199441799
1.7639-1.80490.17822240.1624232445699
1.8049-1.850.18782210.16534188440999
1.85-1.90.19752210.16314215443699
1.9-1.95590.18962230.15954241446499
1.9559-2.01910.18052240.165742504474100
2.0191-2.09120.19792230.155342124435100
2.0912-2.17490.16932220.152542424464100
2.1749-2.27390.19012240.156342594483100
2.2739-2.39380.18712240.160842384462100
2.3938-2.54370.18972240.159842594483100
2.5437-2.740.1742270.168642934520100
2.74-3.01560.18942250.167142704495100
3.0156-3.45170.19462250.166442774502100
3.4517-4.34740.16982280.149643354563100
4.3474-34.91820.18552320.160643954627100

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