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- PDB-7uwt: Structure of Oxygen-Insensitive NAD(P)H-dependent Nitroreductase ... -

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Basic information

Entry
Database: PDB / ID: 7uwt
TitleStructure of Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB_Vv F70A/F108Y (NTR 2.0) in complex with FMN at 1.85 Angstroms resolution
ComponentsDihydropteridine reductase
KeywordsOXIDOREDUCTASE / nitroreductase / flavoenzyme / metronidazole reductase
Function / homology
Function and homology information


6,7-dihydropteridine reductase / oxidoreductase activity
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 / Dihydropteridine reductase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSharrock, A.V. / Arcus, V. / Mumm, J.S. / Ackerley, D.F.
Funding support United States, New Zealand, 3items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR01OD020376 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH126731 United States
Health Research Council (HRC)19-750 New Zealand
CitationJournal: Int J Mol Sci / Year: 2023
Title: The Crystal Structure of Engineered Nitroreductase NTR 2.0 and Impact of F70A and F108Y Substitutions on Substrate Specificity.
Authors: Sharrock, A.V. / Mumm, J.S. / Bagdziunas, G. / Cenas, N. / Arcus, V.L. / Ackerley, D.F.
History
DepositionMay 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,3189
Polymers48,2992
Non-polymers3,0197
Water3,297183
1
A: Dihydropteridine reductase
hetero molecules

A: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3296
Polymers48,2992
Non-polymers1,0314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area8770 Å2
ΔGint-52 kcal/mol
Surface area16810 Å2
MethodPISA
2
B: Dihydropteridine reductase
hetero molecules

B: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,30612
Polymers48,2992
Non-polymers5,00810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8730 Å2
ΔGint-53 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.430, 137.360, 107.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 24149.348 Da / Num. of mol.: 2 / Mutation: F70A,F108Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: FORC53_4366, JS85_12320 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A347SKZ6, 6,7-dihydropteridine reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / 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.: 3 / Source method: obtained synthetically / Formula: C30H62O15
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate trihydrate pH 4.5, PEG 300

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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: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→68.68 Å / Num. obs: 43344 / % possible obs: 99.9 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2625 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DS7

1ds7


Resolution: 1.85→68.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.457 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19625 2177 5 %RANDOM
Rwork0.16467 ---
obs0.16628 41147 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.826 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å2-0 Å2-0 Å2
2---1.27 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.85→68.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 108 183 3637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133520
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173233
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.6584750
X-RAY DIFFRACTIONr_angle_other_deg1.4941.597463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.46922.442172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96215574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.021519
X-RAY DIFFRACTIONr_chiral_restr0.0850.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
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_it1.7121.751736
X-RAY DIFFRACTIONr_mcbond_other1.6591.7471733
X-RAY DIFFRACTIONr_mcangle_it2.2892.6112164
X-RAY DIFFRACTIONr_mcangle_other2.2892.6122165
X-RAY DIFFRACTIONr_scbond_it2.9342.071784
X-RAY DIFFRACTIONr_scbond_other2.9332.0711785
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3432.962587
X-RAY DIFFRACTIONr_long_range_B_refined5.24520.6834118
X-RAY DIFFRACTIONr_long_range_B_other5.24620.6914119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 174 -
Rwork0.201 2999 -
obs--99.69 %

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