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- PDB-6e2a: Crystal structure of NADH:quinone reductase PA1024 from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 6e2a
TitleCrystal structure of NADH:quinone reductase PA1024 from Pseudomonas aeruginosa PAO1 in complex with NAD+
ComponentsNitronate monooxygenase
KeywordsFLAVOPROTEIN / Oxidoreductase / NADH:quinone reductase / quinone / oxidative stress / NAD+ complex
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / nitronate monooxygenase activity / NADH dehydrogenase (quinone) (non-electrogenic) activity / oxidoreductase activity / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH:quinone reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReis, R.A.G. / Ball, J. / Agniswamy, J. / Weber, I. / Gadda, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1506518 United States
CitationJournal: Protein Sci. / Year: 2019
Title: Steric hindrance controls pyridine nucleotide specificity of a flavin-dependent NADH:quinone oxidoreductase.
Authors: Ball, J. / Reis, R.A.G. / Agniswamy, J. / Weber, I.T. / Gadda, G.
History
DepositionJul 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9945
Polymers35,6901
Non-polymers1,3044
Water2,702150
1
A: Nitronate monooxygenase
hetero molecules

A: Nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,98710
Polymers71,3802
Non-polymers2,6088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9420 Å2
ΔGint-45 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.380, 93.380, 80.760
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-512-

HOH

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Components

#1: Protein Nitronate monooxygenase / Nitroalkane oxidase


Mass: 35689.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA1024 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4V0, nitronate monooxygenase
#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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES at pH 7.0, 4% (v/v) tacsimate at pH 7.0, and 15% (w/v) poly-ethylene glycol methyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→80.76 Å / Num. obs: 21045 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1789 / CC1/2: 0.684 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GJL

2gjl


Resolution: 2.2→40.435 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.63
RfactorNum. reflection% reflection
Rfree0.2026 1124 5.35 %
Rwork0.1559 --
obs0.1583 21018 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→40.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 87 150 2664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072697
X-RAY DIFFRACTIONf_angle_d0.8293683
X-RAY DIFFRACTIONf_dihedral_angle_d11.3182123
X-RAY DIFFRACTIONf_chiral_restr0.052410
X-RAY DIFFRACTIONf_plane_restr0.005490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.30020.30791640.22672420X-RAY DIFFRACTION100
2.3002-2.42140.24131190.20062489X-RAY DIFFRACTION100
2.4214-2.57310.23891520.1662435X-RAY DIFFRACTION100
2.5731-2.77180.22441400.16132436X-RAY DIFFRACTION100
2.7718-3.05060.18441300.14672493X-RAY DIFFRACTION100
3.0506-3.49180.19341000.13852523X-RAY DIFFRACTION100
3.4918-4.39850.15221540.13482506X-RAY DIFFRACTION100
4.3985-40.44150.21071650.15912592X-RAY DIFFRACTION100

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