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- PDB-7z0w: E. coli NfsA bound to NADP+ -

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Basic information

Entry
Database: PDB / ID: 7z0w
TitleE. coli NfsA bound to NADP+
ComponentsOxygen-insensitive NADPH nitroreductase
KeywordsOXIDOREDUCTASE / Oxygen-insensitive NADPH nitroreductase / NADP+ complex
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / cytosol
Similarity search - Function
Flavin oxidoreductase Frp family / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE / FLAVIN MONONUCLEOTIDE / Oxygen-insensitive NADPH nitroreductase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsWhite, S.A. / Grainger, A. / Parr, R. / Day, M.A. / Jarrom, D. / Graziano, A. / Searle, P.F. / Hyde, E.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: Febs Lett. / Year: 2022
Title: The 3D-structure, kinetics and dynamics of the E. coli nitroreductase NfsA with NADP + provide glimpses of its catalytic mechanism.
Authors: White, S.A. / Christofferson, A.J. / Grainger, A.I. / Day, M.A. / Jarrom, D. / Graziano, A.E. / Searle, P.F. / Hyde, E.I.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Oxygen-insensitive NADPH nitroreductase
B: Oxygen-insensitive NADPH nitroreductase
C: Oxygen-insensitive NADPH nitroreductase
D: Oxygen-insensitive NADPH nitroreductase
E: Oxygen-insensitive NADPH nitroreductase
F: Oxygen-insensitive NADPH nitroreductase
G: Oxygen-insensitive NADPH nitroreductase
H: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,37520
Polymers214,6618
Non-polymers4,71412
Water22,8251267
1
A: Oxygen-insensitive NADPH nitroreductase
B: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1106
Polymers53,6652
Non-polymers1,4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-89 kcal/mol
Surface area18270 Å2
2
C: Oxygen-insensitive NADPH nitroreductase
D: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1106
Polymers53,6652
Non-polymers1,4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-87 kcal/mol
Surface area18320 Å2
3
E: Oxygen-insensitive NADPH nitroreductase
F: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5784
Polymers53,6652
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint-87 kcal/mol
Surface area18280 Å2
4
G: Oxygen-insensitive NADPH nitroreductase
H: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5784
Polymers53,6652
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11670 Å2
ΔGint-88 kcal/mol
Surface area18260 Å2
Unit cell
Length a, b, c (Å)96.766, 110.757, 112.250
Angle α, β, γ (deg.)90.000, 103.840, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))
21(CHAIN B AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))
31(CHAIN C AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))
41(CHAIN D AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))
51(CHAIN E AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))
61(CHAIN F AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))
71CHAIN G
81(CHAIN H AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(CHAIN A AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))AA11
12ASPASPASPASP(CHAIN A AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))AA210210
13FMNFMNFMNFMN(CHAIN A AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))AI301
21METMETMETMET(CHAIN B AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))BB11
22ASPASPASPASP(CHAIN B AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))BB210210
23FMNFMNFMNFMN(CHAIN B AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))BJ301
31METMETMETMET(CHAIN C AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))CC11
32ASPASPASPASP(CHAIN C AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))CC210210
33FMNFMNFMNFMN(CHAIN C AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))CM301
41METMETMETMET(CHAIN D AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))DD11
42ASPASPASPASP(CHAIN D AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))DD210210
43FMNFMNFMNFMN(CHAIN D AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))DO301
51METMETMETMET(CHAIN E AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))EE11
52ASPASPASPASP(CHAIN E AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))EE210210
53FMNFMNFMNFMN(CHAIN E AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))EQ301
61METMETMETMET(CHAIN F AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))FF11
62ASPASPASPASP(CHAIN F AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))FF210210
63FMNFMNFMNFMN(CHAIN F AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))FR301
71METMETARGARGCHAIN GGG1 - 2401 - 240
81METMETMETMET(CHAIN H AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))HH11
82ASPASPASPASP(CHAIN H AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))HH210210
83FMNFMNFMNFMN(CHAIN H AND (RESID 1 THROUGH 202 OR RESID 210 THROUGH 240 OR RESID 301))HT301

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Components

#1: Protein
Oxygen-insensitive NADPH nitroreductase / Modulator of drug activity A


Mass: 26832.664 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: nfsA, mda18, mdaA, ybjB, b0851, JW0835 / Plasmid: pPS1341A1 / Details (production host): pET24 derivative / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P17117, Oxidoreductases, FMN reductase (NADPH)
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ATR / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1267 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Imidazole, pH 7.6, 20% PEG 6000, 200 mM Magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F5V

1f5v


Resolution: 2.06→81.45 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 6964 4.9 %
Rwork0.153 135159 -
obs0.155 142123 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.76 Å2 / Biso mean: 42.19 Å2 / Biso min: 14.21 Å2
Refinement stepCycle: final / Resolution: 2.06→81.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14943 0 312 1267 16522
Biso mean--35.54 41.29 -
Num. residues----1899
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A9139X-RAY DIFFRACTIONPOSITIONAL0
12B9139X-RAY DIFFRACTIONPOSITIONAL0
13C9139X-RAY DIFFRACTIONPOSITIONAL0
14D9139X-RAY DIFFRACTIONPOSITIONAL0
15E9139X-RAY DIFFRACTIONPOSITIONAL0
16F9139X-RAY DIFFRACTIONPOSITIONAL0
17G9139X-RAY DIFFRACTIONPOSITIONAL0
18H9139X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.06-2.07940.26562210.23154479100
2.0794-2.10380.25052200.22694548100
2.1038-2.12950.26742470.21194459100
2.1295-2.15640.25612400.21124517100
2.1564-2.18480.25932310.20414435100
2.1848-2.21480.24082380.20194528100
2.2148-2.24640.25242300.19544504100
2.2464-2.27990.26152330.19254465100
2.2799-2.31560.21212360.18674538100
2.3156-2.35350.23912560.17254491100
2.3535-2.39410.18862400.15954478100
2.3941-2.43760.20912020.16474523100
2.4376-2.48450.20682190.16314553100
2.4845-2.53530.19422520.16514495100
2.5353-2.59040.23932470.16254476100
2.5904-2.65060.18742330.15634488100
2.6506-2.71690.21332050.15914545100
2.7169-2.79040.18552060.14784546100
2.7904-2.87250.18472530.14724476100
2.8725-2.96520.19762370.15764490100
2.9652-3.07120.19611950.15874557100
3.0712-3.19420.18892240.16084516100
3.1942-3.33960.19622290.15364538100
3.3396-3.51560.19632310.1514449199
3.5156-3.73590.16192410.1427448999
3.7359-4.02430.17172660.1297445399
4.0243-4.42930.13232190.1142448998
4.4293-5.07020.13362390.1126452399
5.0702-6.38750.19042260.1445454099
6.3875-81.4510.1572480.1553452998
Refinement TLS params.Method: refined / Origin x: 106.3267 Å / Origin y: 1.5164 Å / Origin z: 75.2351 Å
111213212223313233
T0.1302 Å2-0.0031 Å2-0.0111 Å2-0.1529 Å20.0033 Å2--0.1516 Å2
L0.0417 °20.0445 °2-0.0351 °2-0.1795 °20.0359 °2--0.1562 °2
S-0.0245 Å °0.0031 Å °-0.0058 Å °0.0007 Å °0.0441 Å °-0.0225 Å °0.012 Å °-0.0121 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 240
2X-RAY DIFFRACTION1ALLA301 - 580
3X-RAY DIFFRACTION1ALLB1 - 240
4X-RAY DIFFRACTION1ALLB301 - 553
5X-RAY DIFFRACTION1ALLC1 - 240
6X-RAY DIFFRACTION1ALLC301 - 590
7X-RAY DIFFRACTION1ALLD1 - 240
8X-RAY DIFFRACTION1ALLD301 - 583
9X-RAY DIFFRACTION1ALLE1 - 240
10X-RAY DIFFRACTION1ALLE301 - 526
11X-RAY DIFFRACTION1ALLF1 - 240
12X-RAY DIFFRACTION1ALLF301 - 527
13X-RAY DIFFRACTION1ALLG1 - 240
14X-RAY DIFFRACTION1ALLG301 - 548
15X-RAY DIFFRACTION1ALLH1 - 240
16X-RAY DIFFRACTION1ALLH301 - 568

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