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- PDB-4eo3: Peroxiredoxin Nitroreductase Fusion Enzyme -

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Basic information

Entry
Database: PDB / ID: 4eo3
TitlePeroxiredoxin Nitroreductase Fusion Enzyme
ComponentsBacterioferritin comigratory protein/NADH dehydrogenase
KeywordsOXIDOREDUCTASE / thioredoxin-fold / alpha-beta-aplha sandwich fold / antioxidant oxidoreductase / FMN Binding
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity / nucleotide binding
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Bacterioferritin comigratory protein/NADH dehydrogenase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 Å
AuthorsProsper, P. / Haouz, A. / Navaza, A. / Jacquot, J.-P. / Rouhier, N.
CitationJournal: Antioxid Redox Signal / Year: 2013
Title: In the absence of thioredoxins, what are the reductants for peroxiredoxins in Thermotoga maritima?
Authors: Couturier, J. / Prosper, P. / Winger, A.M. / Hecker, A. / Hirasawa, M. / Knaff, D.B. / Gans, P. / Jacquot, J.P. / Navaza, A. / Haouz, A. / Rouhier, N.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterioferritin comigratory protein/NADH dehydrogenase
B: Bacterioferritin comigratory protein/NADH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0219
Polymers74,6062
Non-polymers1,4157
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-120 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.500, 113.175, 121.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bacterioferritin comigratory protein/NADH dehydrogenase / Peroxiredoxin nitroreductase


Mass: 37302.840 Da / Num. of mol.: 2 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0386 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYL7
#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNCOI RESTRICTION ENZYME WAS USED FOR CLONING OF THE FULL-LENGTH SEQUENCE. A CODON FOR AN ALANINE ...NCOI RESTRICTION ENZYME WAS USED FOR CLONING OF THE FULL-LENGTH SEQUENCE. A CODON FOR AN ALANINE HAS BEEN ADDED IN THE PRIMER TO KEEP THE SEQUENCE IN FRAME. THE N-TERMINAL PROTEIN SEQUENCE OF THE RECOMBINANT PROTEIN THUS STARTS WITH MARVKHF INSTEAD OF MRVKHF.

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 30% MPD, 5% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2011
RadiationMonochromator: SI (111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.65→19.9 Å / Num. all: 101195 / Num. obs: 101195 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rmerge(I) obs: 0.63 / Net I/σ(I): 24
Reflection shellResolution: 1.65→1.74 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
AMoREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.649→19.896 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 4863 5 %RANDOM
Rwork0.1777 ---
all0.1792 97348 --
obs0.1792 97348 96.15 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.988 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1575 Å20 Å20 Å2
2---2.2877 Å20 Å2
3---0.1302 Å2
Refinement stepCycle: LAST / Resolution: 1.649→19.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 90 612 5942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065519
X-RAY DIFFRACTIONf_angle_d0.9817471
X-RAY DIFFRACTIONf_dihedral_angle_d12.4612095
X-RAY DIFFRACTIONf_chiral_restr0.075811
X-RAY DIFFRACTIONf_plane_restr0.005953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6495-1.70840.29094140.26188219X-RAY DIFFRACTION86
1.7084-1.77680.26354770.23028607X-RAY DIFFRACTION91
1.7768-1.85760.23064410.20768913X-RAY DIFFRACTION93
1.8576-1.95540.22394780.19539128X-RAY DIFFRACTION96
1.9554-2.07780.2114660.18849347X-RAY DIFFRACTION98
2.0778-2.23810.22724980.18549433X-RAY DIFFRACTION98
2.2381-2.46290.22625040.18089509X-RAY DIFFRACTION99
2.4629-2.81840.19244980.17949639X-RAY DIFFRACTION100
2.8184-3.54770.2095270.17889700X-RAY DIFFRACTION100
3.5477-19.89740.18225600.15419990X-RAY DIFFRACTION100

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