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- PDB-1icu: THE STRUCTURE OF ESCHERICHIA COLI NITROREDUCTASE COMPLEXED WITH N... -

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Basic information

Entry
Database: PDB / ID: 1icu
TitleTHE STRUCTURE OF ESCHERICHIA COLI NITROREDUCTASE COMPLEXED WITH NICOTINIC ACID
ComponentsOXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
KeywordsOXIDOREDUCTASE / alpha-beta
Function / homology
Function and homology information


: / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / membrane / identical protein binding / 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
FLAVIN MONONUCLEOTIDE / NICOTINIC ACID / Oxygen-insensitive NAD(P)H nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLovering, A.L. / Hyde, E.I. / Searle, P.F. / White, S.A.
CitationJournal: 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
DepositionApr 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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

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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)98,06712
Polymers95,7494
Non-polymers2,3188
Water2,504139
1
A: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
B: OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0336
Polymers47,8742
Non-polymers1,1594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-35 kcal/mol
Surface area17100 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)49,0336
Polymers47,8742
Non-polymers1,1594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-35 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.010, 57.620, 116.980
Angle α, β, γ (deg.)90, 103.66, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
OXYGEN-INSENSITIVE NAD(P)H 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: NFSB / Plasmid: PET11C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38489, 1.6.99.7
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-NIO / NICOTINIC ACID / Niacin


Mass: 123.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG8K , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
210 %(w/v)PEG40001reservoir
325 %(w/v)ethylene glycol1reservoir
415 mMnicotinic acid1reservoir
5100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→29.91 Å / Num. all: 611309 / Num. obs: 85582 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 6.7 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.3 / Rsym value: 54.9 / % possible all: 97
Reflection
*PLUS
Num. measured all: 611309

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ICR

1icr


Resolution: 1.8→100 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 -5 %random
Rwork0.226 ---
all-611309 --
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-7.67 Å20 Å2-6.06 Å2
2---4.21 Å20 Å2
3----3.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 160 139 7023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.12
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45 Å2

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