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- PDB-9fd5: flavin reductase ThdF in complex with two bound FADs in space gro... -

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Basic information

Entry
Database: PDB / ID: 9fd5
Titleflavin reductase ThdF in complex with two bound FADs in space group P21
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: 1.31 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
B: Flavin reductase
A: Flavin reductase
C: Flavin reductase
D: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,59512
Polymers81,3114
Non-polymers6,2848
Water12,250680
1
B: Flavin reductase
A: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7986
Polymers40,6552
Non-polymers3,1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-71 kcal/mol
Surface area12710 Å2
MethodPISA
2
C: Flavin reductase
D: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7986
Polymers40,6552
Non-polymers3,1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-69 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.150, 77.370, 75.490
Angle α, β, γ (deg.)90.000, 111.827, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 1.97 Å3/Da / Density % sol: 37.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: B11 Proplex (Molecular Dimensions); 0.1 M HEPES pH 7.0, 15 % (w/v) PEG 4000; 18 mg/mL ThdF (50 mM HEPES pH 7.0, 20 mM NaCl, 1 mM DTT), 1:1800 (mass ratio) elastase added; 300 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: 1.31→70.07 Å / Num. obs: 129944 / % possible obs: 86.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 11.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Net I/σ(I): 16.3
Reflection shellResolution: 1.31→1.37 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6497 / CC1/2: 0.804 / Rpim(I) all: 0.287 / Rrim(I) all: 0.709 / % possible all: 35.6

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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: 1.31→54.07 Å / SU ML: 0.1076 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.2771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1529 6445 4.96 %
Rwork0.1151 123481 -
obs0.117 129926 86.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.02 Å2
Refinement stepCycle: LAST / Resolution: 1.31→54.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 424 680 5892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01096055
X-RAY DIFFRACTIONf_angle_d1.26928457
X-RAY DIFFRACTIONf_chiral_restr0.0903924
X-RAY DIFFRACTIONf_plane_restr0.01381050
X-RAY DIFFRACTIONf_dihedral_angle_d20.65272440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.330.2581370.2169552X-RAY DIFFRACTION11.91
1.33-1.350.2586850.18421523X-RAY DIFFRACTION32.08
1.35-1.360.25631170.16262303X-RAY DIFFRACTION49.26
1.36-1.380.22251390.15112681X-RAY DIFFRACTION56.51
1.38-1.40.19441580.15063012X-RAY DIFFRACTION64.14
1.4-1.420.19981750.14253374X-RAY DIFFRACTION71.21
1.42-1.440.21151690.15243665X-RAY DIFFRACTION77.13
1.44-1.460.2141920.14543840X-RAY DIFFRACTION81.74
1.46-1.480.19282390.14454148X-RAY DIFFRACTION87.04
1.48-1.510.20122360.14084427X-RAY DIFFRACTION94.64
1.51-1.530.17772400.12974587X-RAY DIFFRACTION97.52
1.53-1.560.17162300.12084663X-RAY DIFFRACTION97.92
1.56-1.590.18512720.11674598X-RAY DIFFRACTION97.97
1.59-1.620.15882500.1134627X-RAY DIFFRACTION98.17
1.62-1.660.14392540.11064655X-RAY DIFFRACTION98.51
1.66-1.70.1712420.10844694X-RAY DIFFRACTION99.08
1.7-1.740.15752200.10624728X-RAY DIFFRACTION99.24
1.74-1.780.13992110.10144730X-RAY DIFFRACTION99.3
1.78-1.840.14822390.10164727X-RAY DIFFRACTION99.32
1.84-1.90.1372360.10274680X-RAY DIFFRACTION98.95
1.9-1.960.14782270.10374714X-RAY DIFFRACTION99.08
1.96-2.040.14222660.09914681X-RAY DIFFRACTION99
2.04-2.140.14182610.09544660X-RAY DIFFRACTION98.87
2.14-2.250.13152450.09014668X-RAY DIFFRACTION98.85
2.25-2.390.13292660.1024723X-RAY DIFFRACTION99.24
2.39-2.570.15792490.10734757X-RAY DIFFRACTION99.76
2.57-2.830.14612540.11294732X-RAY DIFFRACTION99.82
2.83-3.240.14362660.11834740X-RAY DIFFRACTION99.82
3.24-4.080.13512370.1134761X-RAY DIFFRACTION99.32
4.09-54.070.15342330.13824831X-RAY DIFFRACTION98.89

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