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- PDB-1ds7: A MINOR FMN-DEPENDENT NITROREDUCTASE FROM ESCHERICHIA COLI B -

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Basic information

Entry
Database: PDB / ID: 1ds7
TitleA MINOR FMN-DEPENDENT NITROREDUCTASE FROM ESCHERICHIA COLI B
ComponentsFMN-DEPENDENT NITROREDUCTASE
KeywordsOXIDOREDUCTASE / NAD(P)H-QUINONE REDUCTASE / FMN / NITROREDUCTASE / FLAVOPROTEIN
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
FLAVIN MONONUCLEOTIDE / Oxygen-insensitive NAD(P)H nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.06 Å
AuthorsParkinson, G. / Skelly, J. / Neidle, S.
CitationJournal: J.Med.Chem. / Year: 2000
Title: Crystal structure of FMN-dependent nitroreductase from Escherichia coli B: a prodrug-activating enzyme.
Authors: Parkinson, G.N. / Skelly, J.V. / Neidle, S.
History
DepositionJan 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: FMN-DEPENDENT NITROREDUCTASE
B: FMN-DEPENDENT NITROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7874
Polymers47,8742
Non-polymers9132
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-50 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.740, 57.740, 275.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FMN-DEPENDENT NITROREDUCTASE / OXYGEN-INSENSITIVE NAD(P)H 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) / Strain: B / Plasmid: PK12 / Production host: Escherichia coli (E. coli) / References: UniProt: P38489, EC: 1.6.99.7
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Peg 8000, potassium phosphate, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG80001reservoir
250 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1993 / Details: MIRROR
RadiationMonochromator: N / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 23317 / % possible obs: 71.3 % / Biso Wilson estimate: 4 Å2 / Rmerge(I) obs: 0.114
Reflection
*PLUS
Highest resolution: 1.85 Å / Num. obs: 24109 / % possible obs: 81 % / Num. measured all: 127222 / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS0.5refinement
PROFILEdata scaling
X-PLORphasing
RefinementResolution: 2.06→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 294380.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1419 6.1 %RANDOM
Rwork0.203 ---
all0.219 24099 --
obs0.208 21042 77.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.24 Å2 / ksol: 0.277 e/Å3
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---1.2 Å20 Å2
3---2.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.06→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 62 218 3648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.16
LS refinement shellResolution: 2.06→2.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 140 6.6 %
Rwork0.284 1990 -
obs--43.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1FMN.PARAMTOPH11.WAT
X-RAY DIFFRACTION2PARAM11.WATTOPH19.PEP
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

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