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- PDB-5w8e: The structure of a CoA-dependent acyl-homoserine lactone synthase... -

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Basic information

Entry
Database: PDB / ID: 5w8e
TitleThe structure of a CoA-dependent acyl-homoserine lactone synthase, BjaI, with the adduct of SAH and IV-CoA
ComponentsAutoinducer synthase
KeywordsBIOSYNTHETIC PROTEIN / acyl-homoserine lactone / coenzyme A / BjaI
Function / homologyADENINE / Chem-SXZ / :
Function and homology information
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsDong, S.-H. / Nair, S.K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular basis for the substrate specificity of quorum signal synthases.
Authors: Dong, S.H. / Frane, N.D. / Christensen, Q.H. / Greenberg, E.P. / Nagarajan, R. / Nair, S.K.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Autoinducer synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9015
Polymers25,1701
Non-polymers7314
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-3 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.270, 91.270, 98.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Autoinducer synthase / BjaI


Mass: 25169.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: AF336_03940 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N0C224

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Non-polymers , 5 types, 218 molecules

#2: Chemical ChemComp-SXZ / (2S)-4-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)-2-[(3-methylbutanoyl)amino]butanoic acid


Mass: 468.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N6O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 4.69 Å3/Da / Density % sol: 73.76 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.0 M sodium chloride, 0.085 M HEPES, pH 7.5, 15% v/v glycerol

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 24, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 41676 / % possible obs: 99.15 % / Redundancy: 6.7 % / Net I/σ(I): 13.7
Reflection shellHighest resolution: 1.8 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.937 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21709 2194 5 %RANDOM
Rwork0.19553 ---
obs0.1966 41676 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.69 Å2-0 Å2
2--0.69 Å2-0 Å2
3----2.23 Å2
Refinement stepCycle: 1 / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 49 214 1977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.972548
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2945224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22622.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54815292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4431522
X-RAY DIFFRACTIONr_chiral_restr0.080.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211471
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 161 -
Rwork0.328 3053 -
obs--100 %

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