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- PDB-1idt: STRUCTURAL STUDIES ON A PRODRUG-ACTIVATING SYSTEM-CB1954 AND FMN-... -

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Basic information

Entry
Database: PDB / ID: 1idt
TitleSTRUCTURAL STUDIES ON A PRODRUG-ACTIVATING SYSTEM-CB1954 AND FMN-DEPENDENT NITROREDUCTASE
ComponentsMINOR FMN-DEPENDENT NITROREDUCTASE
KeywordsOXIDOREDUCTASE / FMN / bioreductive activation / prodrug
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
5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE / FLAVIN MONONUCLEOTIDE / Oxygen-insensitive NAD(P)H nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJohansson, E. / Parkinson, G.N. / Denny, W.A. / Neidle, S.
CitationJournal: J.Med.Chem. / Year: 2003
Title: Studies on the Nitroreductase Prodrug-Activating System. Crystal Structures of Complexes with the Inhibitor Dicoumarol and Dinitrobenzamide Prodrugs and of the Enzyme Active Form.
Authors: Johansson, E. / Parkinson, G.N. / Denny, W.A. / Neidle, S.
History
DepositionApr 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 12, 2018Group: Data collection / Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 FMN 1218 AND CB1 1219 ARE ASSOCIATED WITH CHAIN A. FMN 2218 AND CB1 2219 ARE ASSOCIATED ...HETEROGEN FMN 1218 AND CB1 1219 ARE ASSOCIATED WITH CHAIN A. FMN 2218 AND CB1 2219 ARE ASSOCIATED WITH CHAIN B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MINOR FMN-DEPENDENT NITROREDUCTASE
B: MINOR FMN-DEPENDENT NITROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2916
Polymers47,8742
Non-polymers1,4174
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-41 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.556, 57.556, 266.129
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 MINOR 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) / Gene: NFNB OR NFSI OR NFSB OR NTR OR DPRA OR B0578 / Species (production host): Escherichia coli / Production host: Escherichia coli B (bacteria) / Strain (production host): B / References: UniProt: P38489, 1.6.99.7
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CB1 / 5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE / CB1954 / Tretazicar


Mass: 252.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N4O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.6
Details: PEG 4000, sodium acetate , pH 4.6, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976262 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 3, 2000
RadiationMonochromator: germanium 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976262 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 31534 / Num. obs: 28476 / % possible obs: 90.34 % / Observed criterion σ(F): 0 / Redundancy: 13.14 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 29.76
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.201 / % possible all: 98.7

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DS7

1ds7


Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2685 2814 random
Rwork0.2248 --
all0.2294 31245 -
obs0.2294 31245 -
Displacement parametersBiso mean: 29.2792 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 98 192 3652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006283
X-RAY DIFFRACTIONc_angle_d1.162
X-RAY DIFFRACTIONc_dihedral_angle_d22.09
X-RAY DIFFRACTIONc_improper_angle_d1.16
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2-2.010.3004510.2548X-RAY DIFFRACTION437
2.01-2.030.2847610.2613X-RAY DIFFRACTION539

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