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

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Basic information

Entry
Database: PDB / ID: 6wns
TitleThe structure of a CoA-dependent acyl-homoserine lactone synthase, MesI
ComponentsAcyl-homoserine-lactone synthase
KeywordsTRANSFERASE / acyl-homoserine lactone / coenzyme A / MesI
Function / homologyacyl-homoserine-lactone synthase / N-acyl homoserine lactone synthase activity / Autoinducer synthase / Autoinducer synthase / Autoinducer synthase family profile. / quorum sensing / Acyl-CoA N-acyltransferase / Acyl-homoserine-lactone synthase
Function and homology information
Biological speciesMesorhizobium sp. ORS 3359 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 23, 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

Downloads & links

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Assembly

Deposited unit
A: Acyl-homoserine-lactone synthase


Theoretical massNumber of molelcules
Total (without water)23,1211
Polymers23,1211
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.673, 65.673, 113.539
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

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Components

#1: Protein Acyl-homoserine-lactone synthase / Autoinducer synthesis protein


Mass: 23120.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium sp. ORS 3359 (bacteria) / Gene: MPLA_2130039 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A090F1W4, acyl-homoserine-lactone synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate, pH 6.5, 40% v/v MPD, 5% w/v PEG8000

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Data collection

DiffractionMean temperature: 80 K / 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 12, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.93→56.8 Å / Num. obs: 19634 / % possible obs: 99.8 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 37.9
Reflection shellResolution: 1.93→1.93 Å / Num. unique obs: 1329 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-20001data reduction
XDS1data scaling
PHASER1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W8E

5w8e


Resolution: 1.93→56.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.095 / SU ML: 0.121 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2348 986 5.022 %
Rwork0.2146 --
all0.216 --
obs-19633 99.746 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.755 Å2
Baniso -1Baniso -2Baniso -3
1-0.765 Å2-0 Å2-0 Å2
2--0.765 Å2-0 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.93→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 0 110 1668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131595
X-RAY DIFFRACTIONr_bond_other_d0.0060.0171543
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.6392165
X-RAY DIFFRACTIONr_angle_other_deg1.4811.5713539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6375192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12119.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74615263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2341518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021768
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02378
X-RAY DIFFRACTIONr_nbd_refined0.2680.2329
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.21486
X-RAY DIFFRACTIONr_nbtor_refined0.180.2741
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2740.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.211
X-RAY DIFFRACTIONr_nbd_other0.260.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.26
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0130.21
X-RAY DIFFRACTIONr_mcbond_it2.9223.91777
X-RAY DIFFRACTIONr_mcbond_other2.9213.908775
X-RAY DIFFRACTIONr_mcangle_it4.0335.842966
X-RAY DIFFRACTIONr_mcangle_other4.0315.843966
X-RAY DIFFRACTIONr_scbond_it3.4924.198818
X-RAY DIFFRACTIONr_scbond_other3.494.199819
X-RAY DIFFRACTIONr_scangle_it5.2116.1821199
X-RAY DIFFRACTIONr_scangle_other5.2096.1831200
X-RAY DIFFRACTIONr_lrange_it11.05847.0921828
X-RAY DIFFRACTIONr_lrange_other11.04246.2961794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.9690.301510.2851329X-RAY DIFFRACTION98.3607
1.969-2.0230.324850.2541309X-RAY DIFFRACTION100
2.023-2.0820.253690.2151281X-RAY DIFFRACTION100
2.082-2.1460.234670.2241247X-RAY DIFFRACTION100
2.146-2.2160.207600.2061212X-RAY DIFFRACTION100
2.216-2.2940.213580.2111189X-RAY DIFFRACTION100
2.294-2.380.255740.2131117X-RAY DIFFRACTION100
2.38-2.4770.243460.2061098X-RAY DIFFRACTION100
2.477-2.5870.215570.211048X-RAY DIFFRACTION100
2.587-2.7130.218570.2081014X-RAY DIFFRACTION99.7207
2.713-2.860.313530.211944X-RAY DIFFRACTION99.007
2.86-3.0330.246460.227917X-RAY DIFFRACTION100
3.033-3.2410.239510.228859X-RAY DIFFRACTION100
3.241-3.50.261490.241811X-RAY DIFFRACTION100
3.5-3.8330.24350.222746X-RAY DIFFRACTION100
3.833-4.2830.259290.194691X-RAY DIFFRACTION100
4.283-4.9410.205360.174618X-RAY DIFFRACTION100
4.941-6.040.214260.214526X-RAY DIFFRACTION98.3957
6.04-8.4930.249210.234427X-RAY DIFFRACTION100
8-100.177160.177264X-RAY DIFFRACTION98.2456
Refinement TLS params.Method: refined / Origin x: 4.7251 Å / Origin y: -19.5446 Å / Origin z: -4.8744 Å
111213212223313233
T0.2272 Å20.1942 Å20.0628 Å2-0.2651 Å20.0244 Å2--0.0745 Å2
L4.5952 °2-1.0859 °21.1411 °2-2.4774 °2-0.718 °2--4.0539 °2
S0.1358 Å °0.2535 Å °-0.458 Å °-0.5048 Å °-0.2202 Å °-0.072 Å °0.7583 Å °1.0285 Å °0.0845 Å °
Refinement TLS groupSelection: ALL

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