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- PDB-9l11: Crystal structure of flavin reductase (StnC) complexed with FAD -

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Basic information

Entry
Database: PDB / ID: 9l11
TitleCrystal structure of flavin reductase (StnC) complexed with FAD
ComponentsFMN dependent NADH:quinone oxidoreductase
KeywordsFLAVOPROTEIN / Reductase
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FMN dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsXie, X. / Lin, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21632007 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: A new family of StnC-like pseudo-FMN-preferred reductase components in two-component flavoprotein monooxygenases.
Authors: Xie, X. / Wang, X. / Yang, X. / Ji, S. / Ouyang, X. / Zhou, Z. / Xiao, Z. / Guo, W. / Liang, R. / Huang, T. / Deng, Z. / Zhao, Y.L. / Lin, S.
History
DepositionDec 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN dependent NADH:quinone oxidoreductase
B: FMN dependent NADH:quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3804
Polymers49,8092
Non-polymers1,5712
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-31 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.921, 52.860, 174.854
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 FMN dependent NADH:quinone oxidoreductase / Azo-dye reductase / FMN-dependent NADH-azo compound oxidoreductase / FMN-dependent NADH-azoreductase


Mass: 24904.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / Gene: stnC, azoR / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: L7PH54, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor, FMN-dependent NADH-azoreductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / 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.: 242 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1% w/v Tryptone, 0.001M Sodium azide, 0.05M HEPES sodium pH 7.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 37829 / % possible obs: 97 % / Redundancy: 11.6 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.041 / Rrim(I) all: 0.144 / Χ2: 1.252 / Net I/σ(I): 4.3 / Num. measured all: 440322
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.82-1.8511.41.03917610.750.9260.3121.0860.45193.7
1.85-1.8911.40.8917890.8410.9560.2640.930.47792.2
1.89-1.9212.20.82617710.8680.9640.2350.8590.49693
1.92-1.96120.66517850.9090.9760.190.6930.5193
1.96-211.90.57518020.9270.9810.1660.5990.50693.6
2-2.0511.70.517940.9430.9850.1460.5210.52394.2
2.05-2.110.90.41118360.9550.9880.1240.430.54994.7
2.1-2.1611.50.33518160.9720.9930.0980.350.57695.6
2.16-2.2211.40.28318700.9760.9940.0830.2960.62896.6
2.22-2.2910.80.23818880.9810.9950.0720.2490.64296.7
2.29-2.3711.70.22118800.9870.9970.0640.230.68198.8
2.37-2.4711.60.19819080.9870.9970.0580.2060.71299.1
2.47-2.5811.50.16919470.990.9970.050.1770.74999.3
2.58-2.7211.20.14519410.9910.9980.0440.1520.79499.4
2.72-2.8911.90.12519490.9930.9980.0370.1310.93999.7
2.89-3.1111.70.10719560.9960.9990.0320.1121.04999.9
3.11-3.4312.40.09219570.9920.9980.0270.0961.759100
3.43-3.9211.70.07720040.9930.9980.0240.082.142100
3.92-4.9412.30.06720150.9950.9990.020.072.958100
4.94-5011.40.07521600.980.9950.0240.0796.562100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
PDB_EXTRACTV4.1data extraction
PHASER2.8.3phasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→45.28 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.95 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20493 1803 4.8 %RANDOM
Rwork0.18778 ---
obs0.18862 35954 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.292 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.82→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 106 242 3705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133548
X-RAY DIFFRACTIONr_bond_other_d0.0020.0143382
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.6484862
X-RAY DIFFRACTIONr_angle_other_deg1.541.5727733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1175433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.22418.763194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13415533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5141545
X-RAY DIFFRACTIONr_chiral_restr0.0720.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023958
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02822
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.691.9531741
X-RAY DIFFRACTIONr_mcbond_other1.6661.9511740
X-RAY DIFFRACTIONr_mcangle_it2.4122.9192171
X-RAY DIFFRACTIONr_mcangle_other2.4142.9212172
X-RAY DIFFRACTIONr_scbond_it3.3892.4941807
X-RAY DIFFRACTIONr_scbond_other3.3842.4951804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.423.6162692
X-RAY DIFFRACTIONr_long_range_B_refined8.66825.3634164
X-RAY DIFFRACTIONr_long_range_B_other8.725.1764122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.823→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 126 -
Rwork0.23 2437 -
obs--91.47 %

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