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- PDB-8qes: E coli NfsB with the unnatural amino acid, p-aminoPhe at position 124 -

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Basic information

Entry
Database: PDB / ID: 8qes
TitleE coli NfsB with the unnatural amino acid, p-aminoPhe at position 124
ComponentsOxygen-insensitive NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Nitroreductase / unnatural amino acid p-aminoPhenylalanine
Function / homology
Function and homology information


6,7-dihydropteridine reductase / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / oxidoreductase activity / protein homodimerization activity / identical protein binding / membrane / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NICOTINIC ACID / Oxygen-insensitive NAD(P)H nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsDay, M.A. / White, S.A. / Hyde, E.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: The structure of E coli NfsB nitroreducasr with unnatural amino acids at position 124
Authors: Day, M.A. / White, S.A. / Searle, P.F. / Hyde, E.I.
History
DepositionSep 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxygen-insensitive NAD(P)H nitroreductase
B: Oxygen-insensitive NAD(P)H nitroreductase
C: Oxygen-insensitive NAD(P)H nitroreductase
D: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,01212
Polymers97,6944
Non-polymers2,3188
Water4,414245
1
A: Oxygen-insensitive NAD(P)H nitroreductase
C: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0066
Polymers48,8472
Non-polymers1,1594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-31 kcal/mol
Surface area16850 Å2
MethodPISA
2
B: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules

D: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0066
Polymers48,8472
Non-polymers1,1594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area9560 Å2
ΔGint-32 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.450, 57.960, 116.490
Angle α, β, γ (deg.)90.00, 103.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxygen-insensitive NAD(P)H nitroreductase / Dihydropteridine reductase / FMN-dependent nitroreductase


Mass: 24423.623 Da / Num. of mol.: 4 / Mutation: F124(HOX)
Source method: isolated from a genetically manipulated source
Details: DRWGS remains from cleavage of tag in place of N-terminal Met. Residue 124 of NfsB replaced by p-aminoPhe (HOX)
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5a / Gene: nfsB, dprA, nfnB, nfsI, ntr, b0578, JW0567 / Plasmid: pBAD_NTR_124TAG, pDule-pAF
Details (production host): pBAD encodes NTR with stop codon at position 124; pDule contains a suppressor tRNA and an aminoacyl tRNAsynthetase
Production host: Escherichia coli (E. coli) / Strain (production host): DH10B
References: UniProt: P38489, Oxidoreductases, 6,7-dihydropteridine reductase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Sodium acetate, pH 4.6, 15 mM nicotinic acid, 15% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.48→53.81 Å / Num. obs: 32949 / % possible obs: 99.6 % / Redundancy: 3.44 % / Biso Wilson estimate: 14.16 Å2 / Rsym value: 0.094 / Net I/σ(I): 11.5
Reflection shellResolution: 2.48→2.548 Å / Num. unique obs: 2264 / Rsym value: 0.26 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→53.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.505 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.726 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20989 1991 6 %RANDOM
Rwork0.16148 ---
obs0.16442 30944 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.997 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å2-0 Å2-0.6 Å2
2---0.22 Å20 Å2
3----1.09 Å2
Refinement stepCycle: 1 / Resolution: 2.48→53.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6712 0 160 245 7117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0127067
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166616
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.6429603
X-RAY DIFFRACTIONr_angle_other_deg0.6311.58115267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.916532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.343101177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021534
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4642.293477
X-RAY DIFFRACTIONr_mcbond_other3.4612.293477
X-RAY DIFFRACTIONr_mcangle_it4.9994.114348
X-RAY DIFFRACTIONr_mcangle_other4.9984.114349
X-RAY DIFFRACTIONr_scbond_it4.6252.6693590
X-RAY DIFFRACTIONr_scbond_other4.6252.6693589
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7974.6735255
X-RAY DIFFRACTIONr_long_range_B_refined7.90523.868174
X-RAY DIFFRACTIONr_long_range_B_other7.90423.868175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.484→2.548 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 152 -
Rwork0.219 2264 -
obs--99.3 %

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