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- PDB-4n9q: Crystal structure of paAzoR1 bound to ubiquinone-1 -

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Basic information

Entry
Database: PDB / ID: 4n9q
TitleCrystal structure of paAzoR1 bound to ubiquinone-1
ComponentsFMN-dependent NADH-azoreductase 1
KeywordsOXIDOREDUCTASE / azoreductase / quinone / NAD(P)H quinone oxidoreductase / ubiquinone-1
Function / homology
Function and homology information


quinone reductase (NADPH) activity / FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / UBIQUINONE-1 / FMN-dependent NAD(P)H:quinone oxidoreductase 1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsRyan, A. / Kaplan, E. / Crescente, V. / Lowe, E. / Preston, G.M. / Sim, E.
CitationJournal: Plos One / Year: 2014
Title: Identification of NAD(P)H Quinone Oxidoreductase Activity in Azoreductases from P. aeruginosa: Azoreductases and NAD(P)H Quinone Oxidoreductases Belong to the Same FMN-Dependent Superfamily of Enzymes.
Authors: Ryan, A. / Kaplan, E. / Nebel, J.C. / Polycarpou, E. / Crescente, V. / Lowe, E. / Preston, G.M. / Sim, E.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: FMN-dependent NADH-azoreductase 1
B: FMN-dependent NADH-azoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5057
Polymers46,1542
Non-polymers1,3515
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-42 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.402, 82.402, 108.472
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FMN-dependent NADH-azoreductase 1 / Azo-dye reductase 1 / FMN-dependent NADH-azo compound oxidoreductase 1


Mass: 23077.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 /PAO1 /1C /PRS 101 /LMG 12228 / Gene: azoR1, PA0785 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plyss
References: UniProt: Q9I5F3, Oxidoreductases; Acting on other nitrogenous compounds as donors

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Non-polymers , 5 types, 161 molecules

#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-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 1.6 M ammonium sulphate, 0.1 M HEPES pH 7.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8726 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→71.362 Å / Num. all: 26575 / Num. obs: 26575 / % possible obs: 90.7 % / Redundancy: 4.7 % / Rsym value: 0.053 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.112.50.4621.7677926870.46264
2.11-2.243.20.3042.3984530950.30478
2.24-2.394.10.2093.41411334530.20992.6
2.39-2.585.50.1514.71934635100.151100
2.58-2.835.50.0947.11805732590.094100
2.83-3.165.50.0659.41622429470.065100
3.16-3.655.40.04612.41418526070.046100
3.65-4.475.30.04112.91182622270.041100
4.47-6.335.20.03914.5927417760.039100
6.33-43.184.80.03415.7489110140.03499

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIXdev_1448refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2V9C

2v9c


Resolution: 2→43.18 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7707 / SU ML: 0.26 / σ(F): 1.36 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1351 5.09 %
Rwork0.1851 --
obs0.1877 26548 90.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.56 Å2 / Biso mean: 49.2038 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 91 156 3185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033211
X-RAY DIFFRACTIONf_angle_d0.7144360
X-RAY DIFFRACTIONf_chiral_restr0.027475
X-RAY DIFFRACTIONf_plane_restr0.003568
X-RAY DIFFRACTIONf_dihedral_angle_d13.1621172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07230.39851090.29391649175861
2.0723-2.15530.3567960.25541962205871
2.1553-2.25340.28061170.23452211232881
2.2534-2.37220.25611300.20952535266592
2.3722-2.52080.24571370.20742774291199
2.5208-2.71540.22991230.201527662889100
2.7154-2.98860.25151750.197627672942100
2.9886-3.42090.22791570.183127842941100
3.4209-4.30930.22131440.160928212965100
4.3093-43.19050.21271630.169129283091100
Refinement TLS params.Method: refined / Origin x: 24.7322 Å / Origin y: -13.6114 Å / Origin z: 11.766 Å
111213212223313233
T0.2848 Å20.0062 Å20.0328 Å2-0.2819 Å20.0139 Å2--0.3053 Å2
L0.7625 °20.0378 °2-0.5088 °2-0.8514 °2-0.0782 °2--0.7153 °2
S0.1501 Å °0.0344 Å °0.0199 Å °0.0528 Å °-0.0406 Å °-0.2221 Å °-0.0706 Å °0.0818 Å °0.0486 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 1213
2X-RAY DIFFRACTION1allB2 - 1213
3X-RAY DIFFRACTION1allA1 - 302
4X-RAY DIFFRACTION1allA1 - 303
5X-RAY DIFFRACTION1allA1 - 485
6X-RAY DIFFRACTION1allA1 - 304

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