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- PDB-4n65: Crystal structure of paAzoR1 bound to anthraquinone-2-sulphonate -

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Basic information

Entry
Database: PDB / ID: 4n65
TitleCrystal structure of paAzoR1 bound to anthraquinone-2-sulphonate
ComponentsFMN-dependent NADH-azoreductase 1
KeywordsOXIDOREDUCTASE / azoreductase / quinone / NAD(P)H quinone oxidoreductase
Function / homology
Function and homology information


NADPH:quinone reductase 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
9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid / FLAVIN MONONUCLEOTIDE / FMN-dependent NAD(P)H:quinone oxidoreductase 1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.816 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 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)47,7359
Polymers46,1542
Non-polymers1,5817
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-80 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.890, 81.890, 109.380
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
11B-546-

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, 285 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-AQN / 9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid


Mass: 288.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8O5S
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 46.38 %
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: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.815→70.919 Å / Num. all: 37894 / Num. obs: 37894 / % possible obs: 94.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 25.63 Å2 / Rsym value: 0.061 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.815-1.93.80.3512.21431237940.35166
1.9-2.015.40.2453.12917554390.245100
2.01-2.155.40.1485.12760151270.148100
2.15-2.325.40.17.32577147850.1100
2.32-2.555.40.08582353443910.085100
2.55-2.855.30.0689.22143640360.068100
2.85-3.295.30.04712.51861335440.04799.9
3.29-4.035.10.04711.81562630410.047100
4.03-5.694.70.0589.11116123730.05899.7
5.69-43.30850.0310.2678113640.0397.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.816→38.346 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8988 / SU ML: 0.17 / σ(F): 0.1 / Phase error: 16.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1851 1895 5.01 %
Rwork0.1624 --
obs0.1635 37808 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.74 Å2 / Biso mean: 31.9552 Å2 / Biso min: 12.75 Å2
Refinement stepCycle: LAST / Resolution: 1.816→38.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 103 278 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113293
X-RAY DIFFRACTIONf_angle_d1.3154483
X-RAY DIFFRACTIONf_chiral_restr0.082484
X-RAY DIFFRACTIONf_plane_restr0.006584
X-RAY DIFFRACTIONf_dihedral_angle_d14.0731197
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 (%)
1.816-1.8610.2848940.22451687178165
1.861-1.91130.22761330.19882579271299
1.9113-1.96760.21311440.166425792723100
1.9676-2.03110.19081340.149926142748100
2.0311-2.10370.18531180.145826402758100
2.1037-2.18790.15951620.142325752737100
2.1879-2.28740.1731190.143226342753100
2.2874-2.4080.1881270.144826202747100
2.408-2.55890.19961380.149726282766100
2.5589-2.75640.19331390.145826142753100
2.7564-3.03370.18931550.153326632818100
3.0337-3.47240.14441340.146926332767100
3.4724-4.37390.15531540.149926782832100
4.3739-38.35490.22451440.20972769291398
Refinement TLS params.Method: refined / Origin x: 24.4137 Å / Origin y: 13.7279 Å / Origin z: 6.6345 Å
111213212223313233
T0.1104 Å20.0015 Å2-0.0058 Å2-0.1278 Å20.0201 Å2--0.1395 Å2
L1.0157 °20.373 °20.217 °2-1.3379 °20.0207 °2--0.8268 °2
S0.0521 Å °-0.0356 Å °-0.0756 Å °0.0118 Å °-0.0438 Å °-0.2783 Å °0.0624 Å °0.045 Å °-0.0076 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 - 305
5X-RAY DIFFRACTION1allB1 - 302
6X-RAY DIFFRACTION1allA - B1 - 546

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