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- PDB-7n2x: The crystal structure of an FMN-dependent NADH:quinone oxidoreduc... -

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Basic information

Entry
Database: PDB / ID: 7n2x
TitleThe crystal structure of an FMN-dependent NADH:quinone oxidoreductase, AzoR from Escherichia coli
ComponentsFMN-dependent NADH:quinone oxidoreductase
KeywordsOXIDOREDUCTASE / FMN / NADH / Azoreductase / AzoR
Function / homology
Function and homology information


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 / Flavoprotein-like superfamily
Similarity search - Domain/homology
2-AMINO-ACRYLIC ACID / FLAVIN MONONUCLEOTIDE / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / FMN-dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsArcinas, A.J. / Fedorov, E. / Kelly, L. / Almo, S.C. / Ghosh, A.
CitationJournal: To Be Published
Title: Uncovering a novel mechanism of enzyme activation in multimeric azoreductases
Authors: Hitchings, R. / Ryan, A. / Arcinas, A.J. / Ghosh, A. / Almo, S.C. / Kelly, L.
History
DepositionMay 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN-dependent NADH:quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1177
Polymers24,2251
Non-polymers8926
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.355, 94.355, 53.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-303-

DHA

21A-495-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 24225.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: azoR, Z2315, ECs2014 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8X9S9, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor, FMN-dependent NADH-azoreductase

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Non-polymers , 5 types, 180 molecules

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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DHA / 2-AMINO-ACRYLIC ACID / 2,3-DIDEHYDROALANINE


Type: peptide linking / Mass: 87.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO2
#5: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M Magnesium Chloride, 0.1 M HEPES pH 7.5, 22 %(w/v) Polyacrylic Acid 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2017 / Details: KB MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→19.83 Å / Num. obs: 26943 / % possible obs: 99.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 23.13 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.65 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.19.1_4122refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V4B

1v4b


Resolution: 1.7→19.83 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 1360 5.05 %
Rwork0.165 --
obs0.167 26916 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 60 174 1761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.2631430.20792509X-RAY DIFFRACTION100
1.76-1.830.21831390.17822506X-RAY DIFFRACTION100
1.83-1.910.20221320.16592498X-RAY DIFFRACTION100
1.91-2.020.21051390.16752518X-RAY DIFFRACTION100
2.02-2.140.20551460.16562505X-RAY DIFFRACTION100
2.14-2.310.18951370.15632562X-RAY DIFFRACTION100
2.31-2.540.17051260.15882547X-RAY DIFFRACTION100
2.54-2.90.20041250.1772574X-RAY DIFFRACTION100
2.9-3.660.18841340.17292600X-RAY DIFFRACTION100
3.66-19.830.17431390.15472737X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35470.07191.10543.0325-0.75792.20660.19610.24310.1277-0.5112-0.21840.4461-0.3349-0.2371-0.03050.27190.1096-0.03570.19930.00180.234114.484940.360715.8583
25.24222.3189-0.13363.8648-0.66669.13330.21670.33250.4155-0.5-0.53591.3676-0.5088-0.94830.01340.8730.2805-0.1540.54080.03280.43412.242144.64623.0222
33.0044-2.27281.43615.2933-1.87342.55340.25410.1737-0.2939-0.4653-0.15580.31490.1998-0.1821-0.09770.16090.021-0.03740.1876-0.04170.172520.408222.589917.3597
47.00444.9599-4.15084.5509-3.34762.601-0.87970.7645-0.9823-0.88340.3748-2.26030.62430.95610.38240.6610.19520.19710.8112-0.04890.650731.69668.50489.8914
51.6704-1.2569-0.12253.08530.8412.96870.25870.3627-0.087-0.4071-0.211-0.02970.05160.2445-0.05230.1510.0693-0.01080.2041-0.01670.121927.107625.633713.7367
61.8104-1.3824-0.14422.6510.83641.01940.25130.19370.3461-0.3555-0.1392-0.2209-0.42610.0917-0.06540.2502-0.00490.05790.15390.05120.197325.802143.804520.0396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:29)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 30:37)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 38:59)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 60:65)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 66:127)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 128:201)

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