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- PDB-8ysb: Crystal structure of DynA1, a putative monoxygenase from Mivromon... -

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Basic information

Entry
Database: PDB / ID: 8ysb
TitleCrystal structure of DynA1, a putative monoxygenase from Mivromonospora chersina.
ComponentsPredicted ester cyclase
KeywordsISOMERASE / Anthraquinone-fused enediyne / two-enzyme system / anthraquinone formation / OXIDOREDUCTASE
Function / homologypolyketide metabolic process / SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / NTF2-like domain superfamily / Predicted ester cyclase
Function and homology information
Biological speciesMicromonospora chersina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYan, X.F. / Huang, H.W. / Gao, Y.G. / Liang, Z.X.
Funding support Singapore, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2019-T2-2-099 Singapore
Ministry of Education (MoE, Singapore)RG108/20 Singapore
CitationJournal: Jacs Au / Year: 2024
Title: An Enzymatic Oxidation Cascade Converts delta-Thiolactone Anthracene to Anthraquinone in the Biosynthesis of Anthraquinone-Fused Enediynes.
Authors: Ma, G.L. / Liu, W.Q. / Huang, H. / Yan, X.F. / Shen, W. / Visitsatthawong, S. / Prakinee, K. / Tran, H. / Fan, X. / Gao, Y.G. / Chaiyen, P. / Li, J. / Liang, Z.X.
History
DepositionMar 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted ester cyclase


Theoretical massNumber of molelcules
Total (without water)15,7091
Polymers15,7091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.976, 84.160, 83.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Predicted ester cyclase / Aklanonic acid methyl ester cyclase AcmA / Putative hydroxylase


Mass: 15708.979 Da / Num. of mol.: 1 / Mutation: D96G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora chersina (bacteria) / Gene: GA0070603_4190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2BM50

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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: 1.94 Å3/Da / Density % sol: 36.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350, 8% Tacsimate pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→42.09 Å / Num. obs: 5586 / % possible obs: 99.7 % / Redundancy: 12.6 % / Biso Wilson estimate: 65.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1066 / Net I/σ(I): 12.26
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 533 / CC1/2: 0.681

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.08 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.8389
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2894 558 10 %
Rwork0.2655 5022 -
obs0.2678 5580 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 0 0 835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073852
X-RAY DIFFRACTIONf_angle_d0.99571159
X-RAY DIFFRACTIONf_chiral_restr0.0643135
X-RAY DIFFRACTIONf_plane_restr0.006148
X-RAY DIFFRACTIONf_dihedral_angle_d16.037299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.31161360.33091225X-RAY DIFFRACTION99.34
2.53-2.90.33961370.32681233X-RAY DIFFRACTION100
2.9-3.650.31281380.29021243X-RAY DIFFRACTION100
3.65-42.080.2711470.24111321X-RAY DIFFRACTION99.93

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