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- PDB-8v5b: Structure of the oxygen-insensitive NAD(P)H-dependent nitroreduct... -

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Basic information

Entry
Database: PDB / ID: 8v5b
TitleStructure of the oxygen-insensitive NAD(P)H-dependent nitroreductase NfsB_Ec F70A/F108Y in complex with FMN
ComponentsDihydropteridine reductase
KeywordsOXIDOREDUCTASE / nitroreductase / flavoprotein / FMN
Function / homology
Function and homology information


oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase activity / nucleotide binding / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / polyethylene glycol / Oxygen-insensitive NAD(P)H nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSharrock, A.V. / Ackerley, D.F. / Arcus, V.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Marsden FundVUW1902 New Zealand
Other private New Zealand
CitationJournal: Int J Mol Sci / Year: 2024
Title: Structural Evaluation of a Nitroreductase Engineered for Improved Activation of the 5-Nitroimidazole PET Probe SN33623.
Authors: Sharrock, A.V. / Mumm, J.S. / Williams, E.M. / Cenas, N. / Smaill, J.B. / Patterson, A.V. / Ackerley, D.F. / Bagdziunas, G. / Arcus, V.L.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydropteridine reductase
B: Dihydropteridine reductase
C: Dihydropteridine reductase
D: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,50418
Polymers95,5084
Non-polymers2,99614
Water9,296516
1
A: Dihydropteridine reductase
C: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,62510
Polymers47,7542
Non-polymers1,8718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-54 kcal/mol
Surface area16820 Å2
MethodPISA
2
B: Dihydropteridine reductase
D: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8798
Polymers47,7542
Non-polymers1,1256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-61 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.220, 95.590, 112.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydropteridine reductase


Mass: 23877.084 Da / Num. of mol.: 4 / Mutation: F70A, F108Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nfsB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A094VLP5

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Non-polymers , 5 types, 530 molecules

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


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H62O15
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: Sodium chloride, sodium acetate trihydrate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 10, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.98→87.22 Å / Num. obs: 66067 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 9.9
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4399 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→72.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.775 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21912 3293 5 %RANDOM
Rwork0.1706 ---
obs0.17296 62693 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.99 Å2-0 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 1.98→72.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 164 516 7332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136926
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176368
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6629399
X-RAY DIFFRACTIONr_angle_other_deg1.4451.59414733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59623.47317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.081151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9941528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021373
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_it1.5681.6213475
X-RAY DIFFRACTIONr_mcbond_other1.5391.6163466
X-RAY DIFFRACTIONr_mcangle_it2.5172.4164327
X-RAY DIFFRACTIONr_mcangle_other2.5172.4174328
X-RAY DIFFRACTIONr_scbond_it1.8911.8273451
X-RAY DIFFRACTIONr_scbond_other1.8911.8273452
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9532.6335073
X-RAY DIFFRACTIONr_long_range_B_refined5.37119.6448335
X-RAY DIFFRACTIONr_long_range_B_other5.37119.6488336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 254 -
Rwork0.229 4565 -
obs--99.96 %

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