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- PDB-8z15: Crystal structure of DiatB-NADP-6-DMAIAOx complex -

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Basic information

Entry
Database: PDB / ID: 8z15
TitleCrystal structure of DiatB-NADP-6-DMAIAOx complex
ComponentsFlavin-dependent monooxygenase
KeywordsOXIDOREDUCTASE / FAD-dependent oxidoreductase
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
: / Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesStreptomyces ardesiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsPeng, M. / Wu, Q.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2024
Title: Bacterial Biosynthesis of Nitrile-Containing Natural Products: Basis for Recognition of Diversified Substrates
Authors: Peng, M. / Wu, Q. / Ma, L. / Teng, Z.J. / Hou, X. / Zhu, H. / Ju, J.
History
DepositionApr 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6304
Polymers46,8591
Non-polymers1,7713
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-9 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.623, 66.623, 374.184
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Flavin-dependent monooxygenase


Mass: 46858.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Streptomyces ardesiacus (285564) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A7T1BYC5. GenBank Accession ...Details: Sequence reference for Streptomyces ardesiacus (285564) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A7T1BYC5. GenBank Accession Number: PP691700 protein_id="WZN32524.1.
Source: (gene. exp.) Streptomyces ardesiacus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7T1BYC5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-A1D7V / (~{N}~{Z})-~{N}-[2-[6-(3-methylbut-2-enyl)-1~{H}-indol-3-yl]ethylidene]hydroxylamine


Mass: 242.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) PEG 4000, 0.1M Tris base/Hydrochloric acid pH8.5, 0.2M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.55→62.36 Å / Num. obs: 17299 / % possible obs: 100 % / Redundancy: 35 % / CC1/2: 0.999 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.041 / Rrim(I) all: 0.243 / Net I/σ(I): 16
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 36.3 % / Rmerge(I) obs: 1.953 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2415 / CC1/2: 0.705 / Rpim(I) all: 0.326 / Rrim(I) all: 1.98 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.552→52.37 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2934 1718 10 %
Rwork0.2643 --
obs0.2673 17171 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.552→52.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 119 29 3403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0553465
X-RAY DIFFRACTIONf_angle_d4.6074741
X-RAY DIFFRACTIONf_dihedral_angle_d12.831984
X-RAY DIFFRACTIONf_chiral_restr0.236512
X-RAY DIFFRACTIONf_plane_restr0.024614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.552-2.62680.39831380.25931243X-RAY DIFFRACTION100
2.6268-2.71160.38481360.26311230X-RAY DIFFRACTION100
2.7116-2.80850.41281400.27261254X-RAY DIFFRACTION100
2.8085-2.92090.3621390.28451242X-RAY DIFFRACTION100
2.9209-3.05380.41721400.26231269X-RAY DIFFRACTION100
3.0538-3.21480.34911400.2471258X-RAY DIFFRACTION100
3.2148-3.41620.321400.2361256X-RAY DIFFRACTION100
3.4162-3.680.3271430.21711295X-RAY DIFFRACTION100
3.68-4.05020.29751420.20611273X-RAY DIFFRACTION100
4.0502-4.6360.30961460.1891319X-RAY DIFFRACTION100
4.636-5.840.31781500.20331343X-RAY DIFFRACTION100
5.84-52.370.29911640.21651475X-RAY DIFFRACTION100

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