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- PDB-8z14: The crystal structure of DiatB-6-DMAT complex -

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Basic information

Entry
Database: PDB / ID: 8z14
TitleThe crystal structure of DiatB-6-DMAT 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 / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesStreptomyces ardesiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.638 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)47,9173
Polymers46,8591
Non-polymers1,0582
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-9 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.816, 66.816, 375.520
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-A1D7R / (2~{S})-2-azanyl-3-[6-(3-methylbut-2-enyl)-1~{H}-indol-3-yl]propanoic acid / 6-dimethylallyl-L-tryptophan


Type: L-peptide linking / Mass: 272.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Potassium/Sodium phosphate pH 6.5

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Data collection

DiffractionMean temperature: 291 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: 2.638→57.19 Å / Num. obs: 15861 / % possible obs: 100 % / Redundancy: 31.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.209 / Net I/σ(I): 17.7
Reflection shellResolution: 2.64→2.78 Å / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2239 / CC1/2: 0.812 / Rpim(I) all: 0.372 / Rrim(I) all: 1.864

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.638→55.3 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2794 779 10.01 %
Rwork0.2213 --
obs0.2269 15752 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.638→55.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 73 38 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153416
X-RAY DIFFRACTIONf_angle_d1.4054665
X-RAY DIFFRACTIONf_dihedral_angle_d23.5411211
X-RAY DIFFRACTIONf_chiral_restr0.069504
X-RAY DIFFRACTIONf_plane_restr0.017611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.638-2.72290.36211370.28431230X-RAY DIFFRACTION100
2.7229-2.82030.34161390.28591251X-RAY DIFFRACTION100
2.8203-2.93320.37021380.27331244X-RAY DIFFRACTION100
2.9332-3.06670.36321410.27591262X-RAY DIFFRACTION100
3.0667-3.22830.30721370.24811247X-RAY DIFFRACTION100
3.2283-3.43060.29721410.23751269X-RAY DIFFRACTION100
3.4306-3.69540.27441430.2311284X-RAY DIFFRACTION100
3.6954-4.06720.25961410.20181271X-RAY DIFFRACTION100
4.0672-4.65540.21471460.18451312X-RAY DIFFRACTION100
4.6554-5.86430.28641490.19721339X-RAY DIFFRACTION100
5.8643-55.2980.25981640.21451467X-RAY DIFFRACTION100

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