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- PDB-1ylr: The structure of E.coli nitroreductase with bound acetate, crysta... -

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Basic information

Entry
Database: PDB / ID: 1ylr
TitleThe structure of E.coli nitroreductase with bound acetate, crystal form 1
ComponentsOxygen-insensitive NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Oxygen-insensitive NAD(P)H nitroreductase
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 / : / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / 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 19, 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 1.3Sep 28, 2016Group: Other
Revision 1.4Aug 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 B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,9056
Polymers47,8742
Non-polymers1,0314
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-50 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.580, 57.580, 263.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1526-

HOH

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Components

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


Mass: 23937.182 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 43.2 %
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: Sep 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→56.25 Å / Num. all: 49614 / Num. obs: 47753 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8 % / Biso Wilson estimate: 18.8 Å2 / Rsym value: 0.107 / Net I/σ(I): 3.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 7068 / Rsym value: 0.403 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ICR

1icr


Resolution: 1.7→56.25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.68 / SU ML: 0.067 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.1 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19775 2540 5.1 %RANDOM
Rwork0.16991 ---
obs0.17135 47464 99.7 %-
all-47612 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.206 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.7 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→56.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 70 603 4035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223504
X-RAY DIFFRACTIONr_bond_other_d0.0010.023133
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9724756
X-RAY DIFFRACTIONr_angle_other_deg0.77737307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4355431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50424.935154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9215587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8641514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
X-RAY DIFFRACTIONr_nbd_refined0.2050.2779
X-RAY DIFFRACTIONr_nbd_other0.1790.23089
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21717
X-RAY DIFFRACTIONr_nbtor_other0.0830.21764
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2435
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1950.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8491.52778
X-RAY DIFFRACTIONr_mcbond_other0.1871.5876
X-RAY DIFFRACTIONr_mcangle_it0.96923470
X-RAY DIFFRACTIONr_scbond_it1.75131619
X-RAY DIFFRACTIONr_scangle_it2.5454.51286
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 199 -
Rwork0.245 3350 -
obs--97.66 %

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