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- PDB-3r6w: paAzoR1 binding to nitrofurazone -

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Basic information

Entry
Database: PDB / ID: 3r6w
TitlepaAzoR1 binding to nitrofurazone
ComponentsFMN-dependent NADH-azoreductase 1
KeywordsOXIDOREDUCTASE / azoreductase / nitrofurazone / P. aeruginosa / nitroreductase / short-flavodoxin
Function / homology
Function and homology information


NADPH:quinone reductase activity / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / oxidoreductase activity, acting on NAD(P)H, NAD(P) 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 / NITROFURAZONE / FMN-dependent NAD(P)H:quinone oxidoreductase 1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.085 Å
AuthorsRyan, A. / Kaplan, K. / Laurieri, N. / Lowe, E. / Sim, E.
CitationJournal: Sci Rep / Year: 2011
Title: Activation of nitrofurazone by azoreductases: multiple activities in one enzyme.
Authors: Ryan, A. / Kaplan, E. / Laurieri, N. / Lowe, E. / Sim, E.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Sep 13, 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

Downloads & links

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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)48,20414
Polymers46,1542
Non-polymers2,05012
Water4,936274
1
A: FMN-dependent NADH-azoreductase 1
B: FMN-dependent NADH-azoreductase 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)96,40828
Polymers92,3084
Non-polymers4,09924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area18540 Å2
ΔGint-80 kcal/mol
Surface area32270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.202, 82.202, 108.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

21B-316-

HOH

31B-343-

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: paO1 / 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, 286 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NFZ / NITROFURAZONE / 5-NITRO-2-FURALDEHYDE SEMICARBAZONE / Nitrofurazone


Mass: 198.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N4O4 / Comment: antibiotic, Antimicrobial*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
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: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.085→27.146 Å / Num. all: 25785 / Num. obs: 25761 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rsym value: 0.067 / Net I/σ(I): 18.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.085-2.145.20.7661927217940.76695.3
2.14-2.25.50.5861.31004318340.586100
2.2-2.265.50.4831.6982018000.483100
2.26-2.335.50.4121.9936217130.41299.9
2.33-2.415.50.3342.3930417020.334100
2.41-2.495.50.2852.8900716430.285100
2.49-2.595.50.2363.3858015720.236100
2.59-2.695.40.1734.6818315030.17399.9
2.69-2.815.40.1375.7786914500.137100
2.81-2.955.40.1047.5773514230.10499.9
2.95-3.115.40.089.7725213330.08100
3.11-3.35.40.05514683612710.055100
3.3-3.525.40.03919.6637511860.039100
3.52-3.815.30.03124.2598111220.031100
3.81-4.175.30.02726.5539410250.02799.9
4.17-4.665.20.02328.448739310.02399.7
4.66-5.3850.0213242348400.02199.7
5.38-6.595.20.02133.437057160.021100
6.59-9.325.10.01639.529565780.01699.8
9.32-27.1464.60.01340.615013250.01396.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIXdev_694refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V9C

2v9c


Resolution: 2.085→27.146 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8925 / SU ML: 0.64 / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1305 5.07 %5% randomly selected data
Rwork0.1607 ---
all0.1629 25726 --
obs0.1629 25726 99.62 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.682 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 115.94 Å2 / Biso mean: 37.2757 Å2 / Biso min: 12.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.9589 Å20 Å20 Å2
2---0.9589 Å20 Å2
3---1.9179 Å2
Refinement stepCycle: LAST / Resolution: 2.085→27.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 137 274 3547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073389
X-RAY DIFFRACTIONf_angle_d0.9834590
X-RAY DIFFRACTIONf_chiral_restr0.068489
X-RAY DIFFRACTIONf_plane_restr0.004602
X-RAY DIFFRACTIONf_dihedral_angle_d14.0841250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.085-2.16850.27061420.21632623276597
2.1685-2.26710.25111300.180926932823100
2.2671-2.38660.21851470.178526812828100
2.3866-2.5360.26381500.171126542804100
2.536-2.73160.21411420.166727302872100
2.7316-3.00620.22971630.157926682831100
3.0062-3.44050.18731540.144327302884100
3.4405-4.33180.1561470.135727552902100
4.3318-27.14850.20171300.171828873017100
Refinement TLS params.Method: refined / Origin x: 57.7227 Å / Origin y: -14.4024 Å / Origin z: 29.564 Å
111213212223313233
T0.1405 Å20.0049 Å20.0056 Å2-0.1374 Å2-0.0299 Å2--0.1354 Å2
L1.4304 °20.054 °20.26 °2-0.9707 °20.2921 °2--1.008 °2
S0.0045 Å °0.0924 Å °-0.2426 Å °0.0109 Å °0.0644 Å °0.0501 Å °0.1054 Å °0.0504 Å °-0.0524 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 1213
2X-RAY DIFFRACTION1allB2 - 1213
3X-RAY DIFFRACTION1allA1 - 213
4X-RAY DIFFRACTION1allA1 - 214
5X-RAY DIFFRACTION1allA1 - 215
6X-RAY DIFFRACTION1allB1 - 213
7X-RAY DIFFRACTION1allA1 - 216
8X-RAY DIFFRACTION1allA - B1 - 274
9X-RAY DIFFRACTION1allA1 - 217
10X-RAY DIFFRACTION1allA1 - 218
11X-RAY DIFFRACTION1allA1 - 219
12X-RAY DIFFRACTION1allB1 - 214
13X-RAY DIFFRACTION1allA1 - 220

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