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- PDB-8z16: Crystal structure of DiatB mutant N57A -

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Basic information

Entry
Database: PDB / ID: 8z16
TitleCrystal structure of DiatB mutant N57A
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: 2.419 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)48,6174
Polymers46,8161
Non-polymers1,8013
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.928, 67.928, 381.657
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: 46815.859 Da / Num. of mol.: 1 / Mutation: N57A
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-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate and 18% 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: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.419→46.595 Å / Num. obs: 21263 / % possible obs: 100 % / Redundancy: 34.39 % / CC1/2: 0.9975 / Rmerge(I) obs: 0.5528 / Rpim(I) all: 0.0941 / Rrim(I) all: 0.561 / Net I/σ(I): 10
Reflection shellResolution: 2.419→2.506 Å / Redundancy: 32.79 % / Rmerge(I) obs: 3.3094 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 1500 / CC1/2: 0.3618 / Rpim(I) all: 0.5768 / Rrim(I) all: 3.3605 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
autoPXdata reduction
autoPXdata processing
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.419→46.595 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3453 1029 4.88 %
Rwork0.26 --
obs0.264 21084 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.419→46.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 121 43 3416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083464
X-RAY DIFFRACTIONf_angle_d1.0554741
X-RAY DIFFRACTIONf_dihedral_angle_d11.6591980
X-RAY DIFFRACTIONf_chiral_restr0.054513
X-RAY DIFFRACTIONf_plane_restr0.009612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.419-2.54640.47291620.42972678X-RAY DIFFRACTION97
2.5464-2.7060.42931530.39272794X-RAY DIFFRACTION100
2.706-2.91490.48931330.35442807X-RAY DIFFRACTION100
2.9149-3.20810.38871360.32412840X-RAY DIFFRACTION100
3.2081-3.67220.34551380.27082868X-RAY DIFFRACTION100
3.6722-4.62590.32881500.21952909X-RAY DIFFRACTION100
4.6259-46.5950.28631570.20323159X-RAY DIFFRACTION99

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