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- PDB-2fz5: Solution structure of two-electron reduced Megasphaera elsdenii f... -

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Basic information

Entry
Database: PDB / ID: 2fz5
TitleSolution structure of two-electron reduced Megasphaera elsdenii flavodoxin
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / alpha/beta doubly-wound topology / non-covalently bound FMN
Function / homology
Function and homology information


FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FNR / Flavodoxin
Similarity search - Component
Biological speciesMegasphaera elsdenii (bacteria)
MethodSOLUTION NMR / restrained molecular dynamics
Authorsvan Mierlo, C.P.M. / Lijnzaad, P. / Vervoort, J. / Mueller, F. / Berendsen, H.J. / de Vlieg, J.
Citation
Journal: Eur.J.Biochem. / Year: 1990
Title: Tertiary structure of two-electron reduced Megasphaera elsdenii flavodoxin and some implications, as determined by two-dimensional 1H NMR and restrained molecular dynamics
Authors: van Mierlo, C.P.M. / Lijnzaad, P. / Vervoort, J. / Mueller, F. / Berendsen, H.J. / de Vlieg, J.
#1: Journal: Eur.J.Biochem. / Year: 1990
Title: Secondary and tertiary structure characteristics of Megasphaera elsdenii flavodoxin in the reduced state as determined by two-dimensional 1H NMR
Authors: van Mierlo, C.P.M. / Mueller, F. / Vervoort, J.
#2: Journal: Eur.J.Biochem. / Year: 1990
Title: A two-dimensional 1H NMR study on Megasphaera elsdenii flavodoxin in the reduced state: sequential assignments
Authors: van Mierlo, C.P.M. / Vervoort, J. / Mueller, F. / Bacher, A.
#3: Journal: Eur.J.Biochem. / Year: 1990
Title: A two-dimensional 1H NMR study on Megasphaera elsdenii flavodoxin in the oxidized state and some comparisons with the two-electron reduced state
Authors: van Mierlo, C.P.M. / van der Sanden, B.P. / van Woensel, P. / Mueller, F. / Vervoort, J.
History
DepositionFeb 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0202
Polymers14,5611
Non-polymers4581
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 3000
RepresentativeModel #1averaging the restrained molecular dynamics trajectory in the range 60-120 ps.

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Components

#1: Protein Flavodoxin /


Mass: 14561.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Megasphaera elsdenii (bacteria) / References: UniProt: P00321
#2: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121double quantum filtered COSY
131NOESY (mixing 200ms)
144NOESY (mixing 50, 100, 150 ms)
151Double Quantum spectra
161Homonuclear Hartmann Hahn transfer spectra
NMR detailsText: NOESY spectra had mixing times 50, 100, 150 and 200 ms. Double Quantum spectra had a delay of 32 ms. Homonuclear Hartmann Hahn transfer spectra (using MLEV-17 composite pulse cycling) had mixing times 10-160 ms

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Sample preparation

Details
Solution-IDContentsSolvent system
16-10 mM protein, potassium phosphate/potassium pyrophosphate 75-200 mM, pH 8.3, 90% H2O, 10% D2O90% H2O/10% D2O
26-10 mM protein, potassium phosphate/potassium pyrophosphate 75-200 mM, pH 8.3, 99.9% D2O99.9% D2O
Sample conditions
Conditions-IDpHTemperature (K)
18.3 303 K
28.3 306 K
38.3 310 K
48.3 314 K
58.3 316 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker WMBrukerWM5001
Bruker AMBrukerAM5002
Bruker AMBrukerAM6003

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Processing

NMR software
NameDeveloperClassification
DISNMRBrukercollection
GROMOSvan Gunsteren and Berendsenstructure solution
GROMOSvan Gunsteren and Berendsenrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
Details: The Xray structure of the semiquinone state of Clostridium MP flavodoxin was used as a starting structure for restrained molecular dynamics (RMD) calculations in vacuo (van Mierlo et al. Eur. ...Details: The Xray structure of the semiquinone state of Clostridium MP flavodoxin was used as a starting structure for restrained molecular dynamics (RMD) calculations in vacuo (van Mierlo et al. Eur. J. Biochem. 194, 185 - 198 (1990)). 509 distance restraints, 293 medium, 216 long-range were used in refinement. One repulsive restraint, between N5H of FMN and NH of E60 was included. RMD run was of 120 ps. During the first 50 ps the force constant was gradually increased to a high value of 4000 kJmol-1nm-2. From 50 ps on, the force constant was kept constant. The time span of 60-120 ps, at a time resolution of 0.02 ps, was used for calculating the average structure. The time-averaged (not energy minimised) structure has a potential energy -2278 +/- 122 kJmol-1, time-averaged sum of all violations is 2.27 nm, largest occuring violation is 66 pm
NMR representativeSelection criteria: averaging the restrained molecular dynamics trajectory in the range 60-120 ps.
NMR ensembleConformers calculated total number: 3000 / Conformers submitted total number: 1

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