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- PDB-1yki: The structure of E. coli nitroreductase bound with the antibiotic... -

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Basic information

Entry
Database: PDB / ID: 1yki
TitleThe structure of E. coli nitroreductase bound with the antibiotic nitrofurazone
ComponentsOxygen-insensitive NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Oxygen-insensitive NAD(P)H nitroreductase
Function / homology
Function and homology information


oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 6,7-dihydropteridine reductase / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / identical protein binding / membrane / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / FLAVIN MONONUCLEOTIDE / NITROFURAZONE / Oxygen-insensitive NAD(P)H nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRace, P.R. / Lovering, A.L. / Green, R.M. / Ossor, A. / White, S.A. / Searle, P.F. / Wrighton, C.J. / Hyde, E.I.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme.
Authors: Race, P.R. / Lovering, A.L. / Green, R.M. / Ossor, A. / White, S.A. / Searle, P.F. / Wrighton, C.J. / Hyde, E.I.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: The Structure of Escherichia coli Nitroreductase Complexed with Nicotinic Acid: Three Crystal Forms at 1.7 A, 1.8 A and 2.4 A Resolution
Authors: Lovering, A.L. / Hyde, E.I. / Searle, P.F. / White, S.A.
History
DepositionJan 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN LIGANDS 1218-1219 ARE ASSOCIATED WITH CHAIN A LIGANDS 2218-2219 ARE ASSOCIATED WITH CHAIN ...HETEROGEN LIGANDS 1218-1219 ARE ASSOCIATED WITH CHAIN A LIGANDS 2218-2219 ARE ASSOCIATED WITH CHAIN B LIGANDS 3218-3219 ARE ASSOCIATED WITH CHAIN C LIGANDS 4218-4220 ARE ASSOCIATED WITH CHAIN D

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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)98,79316
Polymers95,7494
Non-polymers3,04412
Water16,250902
1
A: Oxygen-insensitive NAD(P)H nitroreductase
B: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2617
Polymers47,8742
Non-polymers1,3875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-38 kcal/mol
Surface area16850 Å2
MethodPISA
2
C: Oxygen-insensitive NAD(P)H nitroreductase
D: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5329
Polymers47,8742
Non-polymers1,6577
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-33 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.078, 56.466, 116.085
Angle α, β, γ (deg.)90.00, 103.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 23937.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nfnB, dprA, nfsB, nfsI, ntr / Plasmid: pET11C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38489, 6,7-dihydropteridine reductase

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Non-polymers , 5 types, 914 molecules

#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-NFZ / NITROFURAZONE / 5-NITRO-2-FURALDEHYDE SEMICARBAZONE


Mass: 198.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6N4O4 / Comment: antibiotic, Antimicrobial*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, ethylene glycol, nicotinic acid, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 97110 / Num. obs: 97110 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 17.1 Å2 / Rsym value: 0.056 / Net I/σ(I): 8.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 14083 / Rsym value: 0.118 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ICU

1icu


Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.44 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16685 4855 5 %RANDOM
Rwork0.14373 ---
obs0.1449 92255 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20.04 Å2
2--0.29 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 205 902 7831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0217073
X-RAY DIFFRACTIONr_bond_other_d0.0020.026280
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9769594
X-RAY DIFFRACTIONr_angle_other_deg0.804314644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635862
X-RAY DIFFRACTIONr_chiral_restr0.0690.21063
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027870
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021370
X-RAY DIFFRACTIONr_nbd_refined0.2040.21533
X-RAY DIFFRACTIONr_nbd_other0.2420.27428
X-RAY DIFFRACTIONr_nbtor_other0.0820.23839
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2679
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.233
X-RAY DIFFRACTIONr_mcbond_it0.4861.54323
X-RAY DIFFRACTIONr_mcangle_it0.91826939
X-RAY DIFFRACTIONr_scbond_it1.59732750
X-RAY DIFFRACTIONr_scangle_it2.6044.52655
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 368
Rwork0.165 6766

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