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- PDB-8ik2: RhlA exhibits dual thioesterase and acyltransferase activities du... -

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Basic information

Entry
Database: PDB / ID: 8ik2
TitleRhlA exhibits dual thioesterase and acyltransferase activities during rhamnolipid biosynthesis
Components3-(3-hydroxydecanoyloxy)decanoate synthase
KeywordsHYDROLASE / thioesterase / acyltransferase / rhamnolipid biosynthesis
Function / homologyrhamnolipid biosynthesis / : / acyltransferase activity / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Alpha/Beta hydrolase fold / (3~{S})-3-oxidanyldecanoic acid / 3-(3-hydroxydecanoyloxy)decanoate synthase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.151 Å
AuthorsTang, T. / Fu, L.H. / Xie, W.H. / Luo, Y.Z. / Zhang, Y.T. / Si, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071428 China
CitationJournal: Acs Catalysis / Year: 2023
Title: RhlA Exhibits Dual Thioesterase and Acyltransferase Activities during Rhamnolipid Biosynthesis
Authors: Tang, T. / Fu, L. / Xie, W. / Luo, Y. / Zhang, Y. / Zhang, J. / Si, T.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-(3-hydroxydecanoyloxy)decanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0272
Polymers33,8391
Non-polymers1881
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.629, 63.890, 85.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-(3-hydroxydecanoyloxy)decanoate synthase


Mass: 33838.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: rhlA, PA3479 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q51559, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-5UF / (3~{S})-3-oxidanyldecanoic acid / Myrmicacin / 3-hydroxydecanoic acid


Mass: 188.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.15→19.76 Å / Num. obs: 27004 / % possible obs: 99.43 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 20.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.099 / Num. unique obs: 27004 / % possible all: 99.43

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.151→19.757 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 2706 10.02 %
Rwork0.1601 --
obs0.164 27004 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→19.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 13 203 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062170
X-RAY DIFFRACTIONf_angle_d0.8672931
X-RAY DIFFRACTIONf_dihedral_angle_d8.0531297
X-RAY DIFFRACTIONf_chiral_restr0.051331
X-RAY DIFFRACTIONf_plane_restr0.005381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.151-2.190.2641210.21161094X-RAY DIFFRACTION85
2.19-2.23210.21431460.1721320X-RAY DIFFRACTION100
2.2321-2.27760.25621440.16081286X-RAY DIFFRACTION100
2.2776-2.3270.21871410.16471293X-RAY DIFFRACTION100
2.327-2.3810.21951470.16291293X-RAY DIFFRACTION100
2.381-2.44050.21941440.16391289X-RAY DIFFRACTION100
2.4405-2.50630.26341460.17391291X-RAY DIFFRACTION100
2.5063-2.57990.25661400.17291265X-RAY DIFFRACTION100
2.5799-2.6630.23871470.18471298X-RAY DIFFRACTION100
2.663-2.7580.2671460.16671260X-RAY DIFFRACTION100
2.758-2.86810.20511460.16111302X-RAY DIFFRACTION100
2.8681-2.99820.22931400.17721268X-RAY DIFFRACTION100
2.9982-3.15570.20321440.16841304X-RAY DIFFRACTION100
3.1557-3.35250.20471380.16681301X-RAY DIFFRACTION100
3.3525-3.60990.16611450.14981285X-RAY DIFFRACTION100
3.6099-3.97050.14841460.13331287X-RAY DIFFRACTION100
3.9705-4.53890.15071440.13351270X-RAY DIFFRACTION100
4.5389-5.69580.17951440.15511301X-RAY DIFFRACTION100
5.6958-19.7570.15561370.15841291X-RAY DIFFRACTION100

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