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- PDB-3p2f: Crystal structure of TofI in an apo form -

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Basic information

Entry
Database: PDB / ID: 3p2f
TitleCrystal structure of TofI in an apo form
ComponentsAHL synthase
KeywordsSIGNALING PROTEIN / synthase / acyl-ACP binding / SAM binding
Function / homology
Function and homology information


acyl-homoserine-lactone synthase / N-acyl homoserine lactone synthase activity / quorum sensing / signal transduction
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
Acyl-homoserine-lactone synthase
Similarity search - Component
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AHL synthase


Theoretical massNumber of molelcules
Total (without water)22,2191
Polymers22,2191
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.971, 65.971, 104.768
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 58.47 % / Mosaicity: 0.407 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 20mM MgCl2, 24% 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: 6C1 / Wavelength: 1.2398 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 20, 2009
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 12209 / Num. obs: 12241 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.079 / Χ2: 1.048 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3410.90.2586131.061100
2.34-2.3810.70.2415921.0181100
2.38-2.4310.90.2336001.0171100
2.43-2.4810.90.2175971.0431100
2.48-2.5310.90.2045951.0231100
2.53-2.5910.80.1725991.0751100
2.59-2.6610.90.1615951.0871100
2.66-2.7310.90.1536091.0411100
2.73-2.8110.90.1315911.0931100
2.81-2.910.80.1226031.1141100
2.9-310.80.1126211.0921100
3-3.1210.90.0945961.1031100
3.12-3.2610.80.0816161.1211100
3.26-3.4410.80.0696161.0841100
3.44-3.6510.80.0646071.1341100
3.65-3.9310.70.0576041.0371100
3.93-4.3310.70.0516300.9561100
4.33-4.9510.60.0486310.961100
4.95-6.2410.30.0526320.9451100
6.24-509.50.0456940.9651100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.61 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 1187 9.7 %RANDOM
Rwork0.2285 ---
all-12624 --
obs-11437 93.7 %-
Solvent computationBsol: 33.1393 Å2
Displacement parametersBiso max: 53.63 Å2 / Biso mean: 24.0044 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å2-3.249 Å20 Å2
2---3.38 Å20 Å2
3---6.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 0 73 1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_d1.2582
X-RAY DIFFRACTIONc_mcbond_it1.2761.5
X-RAY DIFFRACTIONc_scbond_it2.3412
X-RAY DIFFRACTIONc_mcangle_it2.0462
X-RAY DIFFRACTIONc_scangle_it3.3092.5
LS refinement shellResolution: 2.3→2.34 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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