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- PDB-1v5z: Binding of coumarins to NAD(P)H:FMN oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 1v5z
TitleBinding of coumarins to NAD(P)H:FMN oxidoreductase
ComponentsMajor NAD(P)H-flavin oxidoreductase
KeywordsOXIDOREDUCTASE / FMN oxidoreductase / inhibitor / o-coumaric acid / 4-hydroxycoumarin
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / bioluminescence / oxidoreductase activity
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
(2E)-3-(2-HYDROXYPHENYL)ACRYLIC ACID / FLAVIN MONONUCLEOTIDE / Major NAD(P)H-flavin oxidoreductase
Similarity search - Component
Biological speciesAliivibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsKobori, T. / Koike, H. / Sasaki, H. / Zenno, S. / Saigo, K. / Tanokura, M.
CitationJournal: To be Published
Title: Binding of coumarins to NAD(P)H:FMN oxidoreductase
Authors: Kobori, T. / Koike, H. / Sasaki, H. / Zenno, S. / Saigo, K. / Tanokura, M.
History
DepositionNov 26, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: Major NAD(P)H-flavin oxidoreductase
B: Major NAD(P)H-flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4916
Polymers49,2502
Non-polymers1,2414
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-42 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.60, 63.30, 74.40
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Major NAD(P)H-flavin oxidoreductase / FRASE I / NAD(P)H:FMN oxidoreductase


Mass: 24624.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliivibrio fischeri (bacteria) / Gene: FRaseI / Production host: Escherichia coli (E. coli)
References: UniProt: P46072, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#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-2HC / (2E)-3-(2-HYDROXYPHENYL)ACRYLIC ACID / TRANS-2-HYDROXYCINNAMIC ACID / O-COUMARIC ACID / O-Coumaric acid


Mass: 164.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12831
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory BL-6B21
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
X-PLORrefinement
DMphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→10 Å / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.201 / Rfactor obs: 0.201
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 86 160 3714

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