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- PDB-3p2h: Crystal structure of TofI in a ternary complex with an inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 3p2h
TitleCrystal structure of TofI in a ternary complex with an inhibitor and MTA
ComponentsAHL synthase
KeywordsSIGNALING PROTEIN/Inhibitor / synthase / acyl-ACP binding / SAM binding / SIGNALING PROTEIN-Inhibitor-MTA complex / SIGNALING PROTEIN-Inhibitor complex
Function / homology
Function and homology information


acyl-homoserine-lactone synthase / N-acyl homoserine lactone synthase activity / quorum sensing
Similarity search - Function
Autoinducer synthesis, conserved site / Autoinducer synthase family signature. / Autoinducer synthase / Autoinducer synthase / Autoinducer synthase family profile. / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / N-(3-oxocyclohex-1-en-1-yl)octanamide / Acyl-homoserine-lactone synthase
Similarity search - Component
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYu, S. / Rhee, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Small-molecule inhibitor binding to an N-acyl-homoserine lactone synthase
Authors: Chung, J. / Goo, E. / Yu, S. / Choi, O. / Lee, J. / Kim, J. / Kim, H. / Igarashi, J. / Suga, H. / Moon, J.S. / Hwang, I. / Rhee, S.
History
DepositionOct 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AHL synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7543
Polymers22,2191
Non-polymers5352
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.100, 66.100, 104.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein AHL synthase / Acyl homoserine lactone synthase


Mass: 22219.258 Da / Num. of mol.: 1 / Mutation: F42M, I149M, L152M, deletion H91, deletion P92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia glumae (bacteria) / Gene: tofI / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q4VSJ8
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Chemical ChemComp-NOO / N-(3-oxocyclohex-1-en-1-yl)octanamide


Mass: 237.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 20mM MgCl2, 21% polyacrylic acid 5100, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2009
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 25028 / Num. obs: 25136 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.107
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.601 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.05 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1629 8.9 %RANDOM
Rwork0.1998 ---
obs0.2087 16457 87.4 %-
all-24015 --
Solvent computationBsol: 35.4087 Å2
Displacement parametersBiso mean: 21.4197 Å2
Baniso -1Baniso -2Baniso -3
1--2.443 Å2-3.265 Å20 Å2
2---2.443 Å20 Å2
3---4.885 Å2
Refinement stepCycle: LAST / Resolution: 2→33.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 37 95 1577
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.283
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.0091.5
X-RAY DIFFRACTIONc_scbond_it1.7122
X-RAY DIFFRACTIONc_mcangle_it1.5242
X-RAY DIFFRACTIONc_scangle_it2.532.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3inb_mta.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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