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- PDB-9fd4: flavin reductase ThdF in complex with two bound FADs in space gro... -

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Basic information

Entry
Database: PDB / ID: 9fd4
Titleflavin reductase ThdF in complex with two bound FADs in space group P212121
ComponentsFlavin reductase
KeywordsFLAVOPROTEIN / flavin reductase / FAD / oxidoreductase / NADH:FAD oxdioreductase
Function / homology: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / riboflavin reductase (NADPH) activity / FMN-binding split barrel / FMN binding / FLAVIN-ADENINE DINUCLEOTIDE / Flavin reductase
Function and homology information
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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

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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)88,18019
Polymers81,3114
Non-polymers6,86915
Water10,251569
1
A: Flavin reductase
B: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,22811
Polymers40,6552
Non-polymers3,5739
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-77 kcal/mol
Surface area12690 Å2
MethodPISA
2
C: Flavin reductase
D: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9528
Polymers40,6552
Non-polymers3,2966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-70 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.790, 83.610, 157.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
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

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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: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.14→57.3 Å / Num. obs: 188862 / % possible obs: 82.4 % / Redundancy: 35.2 % / Biso Wilson estimate: 16.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.015 / Rrim(I) all: 0.089 / Net I/σ(I): 21.5
Reflection shellResolution: 1.14→1.22 Å / Rmerge(I) obs: 2.19 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 9443 / CC1/2: 0.624 / Rpim(I) all: 0.469 / Rrim(I) all: 2.242 / % possible all: 22.5

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSBUILT=20220220data reduction
STARANISOserver release v3.351 25-Oct-2023data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→57.29 Å / SU ML: 0.1029 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1418 9434 5 %
Rwork0.1209 179364 -
obs0.1219 188798 82.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.74 Å2
Refinement stepCycle: LAST / Resolution: 1.14→57.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4791 0 462 569 5822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01015947
X-RAY DIFFRACTIONf_angle_d1.23668280
X-RAY DIFFRACTIONf_chiral_restr0.0885909
X-RAY DIFFRACTIONf_plane_restr0.01321012
X-RAY DIFFRACTIONf_dihedral_angle_d20.80262398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.3191210.245260X-RAY DIFFRACTION3.75
1.15-1.170.2073480.211971X-RAY DIFFRACTION13.33
1.17-1.180.2191760.2151529X-RAY DIFFRACTION21.47
1.18-1.20.25321000.20052079X-RAY DIFFRACTION28.56
1.2-1.210.22791300.19242437X-RAY DIFFRACTION34.08
1.21-1.230.22841830.20983302X-RAY DIFFRACTION45.85
1.23-1.250.24182330.20794465X-RAY DIFFRACTION62.28
1.25-1.260.22922780.18425484X-RAY DIFFRACTION76.05
1.26-1.280.23163330.19036224X-RAY DIFFRACTION86.4
1.28-1.310.23373400.18316918X-RAY DIFFRACTION96.12
1.31-1.330.20843330.15927231X-RAY DIFFRACTION99.25
1.33-1.350.19463950.13817157X-RAY DIFFRACTION99.89
1.35-1.380.16953910.12487192X-RAY DIFFRACTION99.99
1.38-1.410.19084340.12277200X-RAY DIFFRACTION100
1.41-1.440.16543730.1157216X-RAY DIFFRACTION99.97
1.44-1.470.14213570.11077196X-RAY DIFFRACTION100
1.47-1.510.15163870.10637251X-RAY DIFFRACTION100
1.51-1.550.14434050.09867238X-RAY DIFFRACTION100
1.55-1.590.13193690.09697249X-RAY DIFFRACTION100
1.59-1.650.15543870.10557241X-RAY DIFFRACTION100
1.65-1.70.13493860.10057238X-RAY DIFFRACTION100
1.7-1.770.13754000.09547246X-RAY DIFFRACTION100
1.77-1.850.12673850.09787276X-RAY DIFFRACTION100
1.85-1.950.12043810.09967253X-RAY DIFFRACTION100
1.95-2.070.12813950.10167319X-RAY DIFFRACTION100
2.07-2.230.13523820.09957285X-RAY DIFFRACTION100
2.23-2.460.1343620.10877383X-RAY DIFFRACTION100
2.46-2.810.13113940.12087391X-RAY DIFFRACTION100
2.81-3.540.13183820.12577447X-RAY DIFFRACTION100
3.54-57.290.14193940.14287686X-RAY DIFFRACTION99.17

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