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- PDB-1f5v: STRUCTURE AND SITE-DIRECTED MUTAGENESIS OF A FLAVOPROTEIN FROM ES... -

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Basic information

Entry
Database: PDB / ID: 1f5v
TitleSTRUCTURE AND SITE-DIRECTED MUTAGENESIS OF A FLAVOPROTEIN FROM ESCHERICHIA COLI THAT REDUCES NITROCOMPOUNDS. ALTERATION OF PYRIDINE NUCLEOTIDE BINDING BY A SINGLE AMINO ACID SUBSTITUTION
ComponentsOXYGEN-INSENSITIVE NADPH NITROREDUCTASE
KeywordsOXIDOREDUCTASE / nitroreductase / flavoprotein / Escherichia coli / oxidoreduction / nitrocompound
Function / homology
Function and homology information


chromate reductase activity / : / NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / cytosol
Similarity search - Function
Flavin oxidoreductase Frp family / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Oxygen-insensitive NADPH nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsKobori, T. / Sasaki, H. / Lee, W.C. / Zenno, S. / Saigo, K. / Murphy, M.E.P. / Tanokura, M.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structure and site-directed mutagenesis of a flavoprotein from Escherichia coli that reduces nitrocompounds: alteration of pyridine nucleotide binding by a single amino acid substitution.
Authors: Kobori, T. / Sasaki, H. / Lee, W.C. / Zenno, S. / Saigo, K. / Murphy, M.E. / Tanokura, M.
History
DepositionJun 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref.pdbx_seq_one_letter_code / _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 NADPH NITROREDUCTASE
B: OXYGEN-INSENSITIVE NADPH NITROREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5784
Polymers53,6652
Non-polymers9132
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-84 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.560, 52.860, 52.830
Angle α, β, γ (deg.)75.79, 60.71, 61.17
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein OXYGEN-INSENSITIVE NADPH NITROREDUCTASE


Mass: 26832.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PAJ102 / Production host: Escherichia coli (E. coli) / References: UniProt: P17117, EC: 1.6.99.6
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0539.97
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2811vapor diffusion, sitting drop6.5PEG 6000, MES, sodium hydroxide, PEG 400, dioxane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 281.0K
2812vapor diffusion, sitting drop6.5PEG 6000, MES, sodium hydroxide, PEG 400, dioxane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 281.0K
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122.5 %PEG60001reservoir
22-15 %PEG4001reservoir
3100 mMMES1reservoir
49 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONPhoton Factory BL-6A21
Detector
TypeIDDetectorDate
RIGAKU RAXIS IIC1IMAGE PLATE
FUJI2IMAGE PLATENov 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 41935 / % possible obs: 91.8 % / Rmerge(I) obs: 0.033

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→7 Å
RfactorNum. reflectionSelection details
Rfree0.206 -RANDOM
Rwork0.189 --
obs-42534 -
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 62 349 4185
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.69
Software
*PLUS
Name: 'X-PLOR 3.1, CNS' / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 7 Å / % reflection Rfree: 5 % / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.918
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.759

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