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- PDB-8z12: Crystal structure of WT DiatB -

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Basic information

Entry
Database: PDB / ID: 8z12
TitleCrystal structure of WT DiatB
ComponentsFlavin-dependent monooxygenase
KeywordsOXIDOREDUCTASE / FAD-dependent oxidoreductase
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide 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 / CITRATE ANION / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesStreptomyces ardesiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.238 Å
AuthorsPeng, M. / Wu, Q.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) 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)47,8343
Polymers46,8591
Non-polymers9752
Water2,702150
1
A: Flavin-dependent monooxygenase
hetero molecules

A: Flavin-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6676
Polymers93,7182
Non-polymers1,9494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area2120 Å2
ΔGint-10 kcal/mol
Surface area36130 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-10 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.846, 66.846, 376.751
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-675-

HOH

31A-716-

HOH

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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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium citrate tribasic tetrahydrate (pH 8.4), 20% (w/v) polyethylene glycol (PEG) 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→62.8 Å / Num. obs: 24232 / % possible obs: 94.7 % / Redundancy: 33.5 % / CC1/2: 1 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.031 / Rrim(I) all: 0.184 / Net I/σ(I): 19
Reflection shellResolution: 2.24→2.36 Å / Rmerge(I) obs: 1.634 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2144 / CC1/2: 0.901 / Rpim(I) all: 0.286 / Rrim(I) all: 1.66 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.238→52.573 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 2000 8.3 %
Rwork0.2048 --
obs0.2085 24097 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.238→52.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 66 150 3471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083407
X-RAY DIFFRACTIONf_angle_d1.0294653
X-RAY DIFFRACTIONf_dihedral_angle_d9.3961979
X-RAY DIFFRACTIONf_chiral_restr0.058503
X-RAY DIFFRACTIONf_plane_restr0.006611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.238-2.2940.2731200.26791317X-RAY DIFFRACTION82
2.294-2.3560.32491440.23281602X-RAY DIFFRACTION100
2.356-2.42530.31951470.23491616X-RAY DIFFRACTION100
2.4253-2.50360.31981450.22951612X-RAY DIFFRACTION100
2.5036-2.59310.2981480.23531638X-RAY DIFFRACTION100
2.5931-2.69690.28881150.23331261X-RAY DIFFRACTION78
2.6969-2.81960.3231480.23271641X-RAY DIFFRACTION100
2.8196-2.96830.26841480.23721638X-RAY DIFFRACTION100
2.9683-3.15420.27341500.23621661X-RAY DIFFRACTION100
3.1542-3.39770.25381510.22011665X-RAY DIFFRACTION100
3.3977-3.73960.25841210.20841331X-RAY DIFFRACTION79
3.7396-4.28050.19941330.17371477X-RAY DIFFRACTION87
4.2805-5.39210.20151580.16671735X-RAY DIFFRACTION100
5.3921-52.5730.2291720.18971903X-RAY DIFFRACTION100

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