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- PDB-9fd6: flavin reductase ThdF in complex with NAD and FAD -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9fd6
Titleflavin reductase ThdF in complex with NAD and FAD
ComponentsFlavin reductase
KeywordsFLAVOPROTEIN / flavin reductase / FAD / oxidoreductase / NADH:FAD oxdioreductase
Function / homology
Function and homology information


riboflavin reductase (NADPH) activity / FMN binding
Similarity search - Function
: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / FMN-binding split barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Flavin reductase
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.43 Å
AuthorsBork, S. / Nagel, M.F. / Keller, W. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 694/10-1 Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The NADH-dependent flavin reductase ThdF follows an ordered sequential mechanism though crystal structures reveal two FAD molecules in the active site.
Authors: Horstmeier, H.J. / Bork, S. / Nagel, M.F. / Keller, W. / Spross, J. / Diepold, N. / Ruppel, M. / Kottke, T. / Niemann, H.H.
History
DepositionMay 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 5, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavin reductase
C: Flavin reductase
B: Flavin reductase
D: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,11512
Polymers81,3114
Non-polymers5,8048
Water11,872659
1
A: Flavin reductase
B: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5576
Polymers40,6552
Non-polymers2,9024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-63 kcal/mol
Surface area12720 Å2
MethodPISA
2
C: Flavin reductase
D: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5576
Polymers40,6552
Non-polymers2,9024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-67 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.760, 83.480, 159.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Flavin reductase


Mass: 20327.689 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albogriseolus (bacteria) / Gene: thdF / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B1V585
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 36.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: D12 JCSG++ (Jena Bioscience); 40 mM KH2PO4, 20 % (v/v) glycerol, 16 % (w/v) PEG 8000; 18 mg/mL ThdF (50 mM HEPES pH 7.0, 20 mM NaCl, 1 mM DTT), 1:1800 (mass ratio) elastase added; 600 nL ...Details: D12 JCSG++ (Jena Bioscience); 40 mM KH2PO4, 20 % (v/v) glycerol, 16 % (w/v) PEG 8000; 18 mg/mL ThdF (50 mM HEPES pH 7.0, 20 mM NaCl, 1 mM DTT), 1:1800 (mass ratio) elastase added; 600 nL protein + 300 nL reservoir; soaking with 250 nL 100 mM NADH and 250 nL 500 mM dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.43→73.92 Å / Num. obs: 95935 / % possible obs: 80.3 % / Redundancy: 13.5 % / Biso Wilson estimate: 18.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Net I/σ(I): 14.9
Reflection shellResolution: 1.43→1.55 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.901 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4797 / CC1/2: 0.594 / Rpim(I) all: 0.529 / Rrim(I) all: 1.974 / % possible all: 18.6

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSBUILT=20220820data reduction
STARANISOserver release v3.351 25-Oct-2023data scaling
PHENIX1.21_5207phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.43→45.74 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 4919 5.13 %
Rwork0.1458 --
obs0.1477 95908 80.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4801 0 388 659 5848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055910
X-RAY DIFFRACTIONf_angle_d0.9598239
X-RAY DIFFRACTIONf_dihedral_angle_d21.0912569
X-RAY DIFFRACTIONf_chiral_restr0.068918
X-RAY DIFFRACTIONf_plane_restr0.0081012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.440.261720.318115X-RAY DIFFRACTION0
1.44-1.460.260490.2401130X-RAY DIFFRACTION4
1.46-1.480.3657140.2839231X-RAY DIFFRACTION6
1.48-1.490.2383280.2309559X-RAY DIFFRACTION15
1.49-1.510.3154460.24461002X-RAY DIFFRACTION27
1.51-1.540.2562970.23031517X-RAY DIFFRACTION41
1.54-1.560.25981160.21172090X-RAY DIFFRACTION57
1.56-1.580.24261480.21142713X-RAY DIFFRACTION72
1.58-1.610.28181920.20223148X-RAY DIFFRACTION85
1.61-1.630.2671970.21223629X-RAY DIFFRACTION97
1.63-1.660.26732200.213722X-RAY DIFFRACTION100
1.66-1.690.25392190.1913707X-RAY DIFFRACTION100
1.69-1.720.2152060.17653745X-RAY DIFFRACTION100
1.72-1.760.23741770.1673779X-RAY DIFFRACTION100
1.76-1.80.22231920.15863744X-RAY DIFFRACTION100
1.8-1.840.21361960.14873799X-RAY DIFFRACTION100
1.84-1.880.19561960.13923736X-RAY DIFFRACTION100
1.88-1.930.27261960.15973780X-RAY DIFFRACTION100
1.93-1.990.17392210.14263770X-RAY DIFFRACTION100
1.99-2.060.17591920.13093742X-RAY DIFFRACTION100
2.06-2.130.17152190.12243760X-RAY DIFFRACTION100
2.13-2.210.15681960.11833791X-RAY DIFFRACTION100
2.21-2.310.17471970.13223786X-RAY DIFFRACTION100
2.31-2.440.16892130.12933772X-RAY DIFFRACTION100
2.44-2.590.16822130.1363812X-RAY DIFFRACTION100
2.59-2.790.17271940.13923830X-RAY DIFFRACTION100
2.79-3.070.1861970.14253828X-RAY DIFFRACTION100
3.07-3.510.17091790.13483895X-RAY DIFFRACTION100
3.51-4.430.13732290.12393885X-RAY DIFFRACTION100
4.43-45.740.18092180.16884072X-RAY DIFFRACTION100

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