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- PDB-6wn0: The structure of a CoA-dependent acyl-homoserine lactone synthase... -

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Basic information

Entry
Database: PDB / ID: 6wn0
TitleThe structure of a CoA-dependent acyl-homoserine lactone synthase, RpaI, with the adduct of SAH and p-coumaroyl CoA
Components4-coumaroyl-homoserine lactone synthase
KeywordsTRANSFERASE / acyl-homoserine lactone / coenzyme A / RpaI
Function / homology
Function and homology information


4-coumaroyl-homoserine lactone synthase / quorum sensing / transferase activity
Similarity search - Function
Autoinducer synthase / Autoinducer synthase / Autoinducer synthase family profile. / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / Chem-U4Y / 4-coumaroyl-homoserine lactone synthase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDong, S.-H. / Nair, S.K.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structure-Guided Biochemical Analysis of Quorum Signal Synthase Specificities.
Authors: Dong, S.H. / Nhu-Lam, M. / Nagarajan, R. / Nair, S.K.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-coumaroyl-homoserine lactone synthase
B: 4-coumaroyl-homoserine lactone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8036
Polymers48,2032
Non-polymers2,6004
Water9,026501
1
A: 4-coumaroyl-homoserine lactone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4023
Polymers24,1021
Non-polymers1,3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-coumaroyl-homoserine lactone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4023
Polymers24,1021
Non-polymers1,3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.519, 100.512, 105.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 4-coumaroyl-homoserine lactone synthase / p-coumaryl-homoserine lactone synthase / pC-HSL synthase / RpaI


Mass: 24101.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: rpaI, RPA0320 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6NCZ6, 4-coumaroyl-homoserine lactone synthase
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-U4Y / (2S)-4-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)-2-{[(2E)-3-(cis-4-hydroxycyclohexa-2,5-dien-1-yl)prop-2-enoyl]amino}butanoic acid


Mass: 532.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H28N6O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 11, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 38339 / % possible obs: 97.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Χ2: 0.964 / Net I/σ(I): 5.9 / Num. measured all: 236834
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.8860.76518190.7010.3260.8370.86296.1
1.88-1.9260.65418820.7660.2780.7160.90596.4
1.92-1.9560.55918630.8060.2370.6120.92896.9
1.95-1.9960.46518480.8480.1970.5080.93496.2
1.99-2.045.90.42218830.8730.180.4620.95396.4
2.04-2.085.90.34918490.8910.1490.3820.98196
2.08-2.145.90.29919180.930.1280.3280.95296.6
2.14-2.195.90.26518370.9490.1140.290.96195.8
2.19-2.265.80.22818950.9550.0990.250.94797.2
2.26-2.335.80.20418950.9580.0880.2240.93896.8
2.33-2.415.90.18218850.9730.0780.1990.92897.4
2.41-2.515.90.16519390.9740.0710.180.91297.8
2.51-2.635.90.14219170.9830.0610.1550.92898.4
2.63-2.766.10.13219420.9830.0550.1440.97498.8
2.76-2.946.30.11219450.9890.0450.1211.15299.4
2.94-3.166.60.10119850.9910.040.1091.31299.5
3.16-3.486.90.0819710.9950.030.0861.38299
3.48-3.9970.05319820.9970.020.0570.93198.7
3.99-5.026.90.03819950.9980.0150.0410.71297.7
5.02-506.50.03420890.9990.0130.0370.64296.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W8E

5w8e


Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.535 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.147
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 1880 5 %RANDOM
Rwork0.1866 ---
obs0.1887 35779 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.33 Å2 / Biso mean: 21.701 Å2 / Biso min: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å2-0 Å2
2---0.19 Å20 Å2
3---0.51 Å2
Refinement stepCycle: final / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 170 501 4060
Biso mean--21.13 31.54 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193651
X-RAY DIFFRACTIONr_angle_refined_deg1.4912.0154986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5055423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03622.335167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50715568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2011542
X-RAY DIFFRACTIONr_chiral_restr0.0990.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212788
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 113 -
Rwork0.271 2211 -
all-2324 -
obs--83.06 %

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