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- PDB-4yqe: Crystal structure of E. coli WrbA in complex with benzoquinone -

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Basic information

Entry
Database: PDB / ID: 4yqe
TitleCrystal structure of E. coli WrbA in complex with benzoquinone
ComponentsNAD(P)H dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / Flavin Mononucleotide / NAD(P)H Dehydrogenase (Quinone) / Oxidation-Reduction / Protein Binding / Repressor Proteins
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to oxidative stress / protein-containing complex ...NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to oxidative stress / protein-containing complex / identical protein binding / membrane / cytosol
Similarity search - Function
NAD(P)H dehydrogenase (quinone), prokaryotic / Flavoprotein WrbA-like / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 1,4-benzoquinone / NAD(P)H dehydrogenase (quinone)
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.33 Å
AuthorsDegtjarik, O. / Brynda, J. / Ettrichova, O. / Carey, J. / Kuta Smatanova, I. / Ettrich, R.
CitationJournal: J.Phys.Chem.B / Year: 2016
Title: Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA.
Authors: Degtjarik, O. / Brynda, J. / Ettrichova, O. / Kuty, M. / Sinha, D. / Kuta Smatanova, I. / Carey, J. / Ettrich, R. / Reha, D.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Jun 22, 2016Group: Database references
Revision 1.4Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.5Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6236
Polymers41,4952
Non-polymers1,1294
Water4,035224
1
A: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)
hetero molecules

A: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,24712
Polymers82,9894
Non-polymers2,2588
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13910 Å2
ΔGint-47 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.179, 61.179, 169.992
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
SymmetryPoint symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 197 / Label seq-ID: 1 - 197

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein NAD(P)H dehydrogenase (quinone) / Flavoprotein WrbA / NAD(P)H:quinone oxidoreductase / NQO / NAD(P)H:quinone oxidoreductase


Mass: 20747.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: wrbA, b1004, JW0989 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A8G6, NAD(P)H dehydrogenase (quinone)
#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-PLQ / 1,4-benzoquinone / cyclohexa-2,5-diene-1,4-dione / QUINONE RING OF THE PLASTOQUINONE 9


Mass: 108.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 1.92 Å3/Da / Density % sol: 35.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/Imidazol, 12.5 % PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2014
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.33→42.5 Å / Num. all: 142025 / Num. obs: 141939 / % possible obs: 99.9 % / Redundancy: 5.63 % / Biso Wilson estimate: 20.75 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.02
Reflection shellResolution: 1.33→1.41 Å / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.36 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.552
Highest resolutionLowest resolution
Rotation42.5 Å3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREP11.1.03phasing
PDB_EXTRACT3.15data extraction
XDSXDSAPP 0.21data reduction
Coot0.7.2model building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RG1

2rg1


Resolution: 1.33→42.5 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1608 / WRfactor Rwork: 0.1248 / FOM work R set: 0.931 / SU B: 1.394 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0463 / SU Rfree: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1608 3763 5 %RANDOM
Rwork0.1248 71491 --
obs0.1266 71491 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 136.93 Å2 / Biso mean: 21.479 Å2 / Biso min: 10.61 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.33→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 78 225 3109
Biso mean--20.49 33.36 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193061
X-RAY DIFFRACTIONr_bond_other_d0.0050.022841
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9924195
X-RAY DIFFRACTIONr_angle_other_deg1.11736568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37524.174115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97115467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8971514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213537
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02681
X-RAY DIFFRACTIONr_mcbond_it2.5111.9231562
X-RAY DIFFRACTIONr_mcbond_other2.5021.9221561
X-RAY DIFFRACTIONr_mcangle_it2.9982.8891958
X-RAY DIFFRACTIONr_rigid_bond_restr3.23535901
X-RAY DIFFRACTIONr_sphericity_free28.296564
X-RAY DIFFRACTIONr_sphericity_bonded11.33655982
Refine LS restraints NCS

Ens-ID: 1 / Number: 10228 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.329→1.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 272 -
Rwork0.158 5162 -
all-5434 -
obs--99.62 %

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