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- PDB-1k4j: Crystal Structure of the Acyl-homoserinelactone Synthase EsaI Com... -

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Basic information

Entry
Database: PDB / ID: 1k4j
TitleCrystal Structure of the Acyl-homoserinelactone Synthase EsaI Complexed with Rhenate
Componentsacyl-homoserinelactone synthase EsaI
KeywordsLIGASE / acyl-homoserinelactone synthase / mixed alpha beta / enzyme / GNAT similarity / quorum sensing / autoinducer synthase
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
PERRHENATE / Acyl-homoserine-lactone synthase
Similarity search - Component
Biological speciesPantoea stewartii subsp. stewartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsWatson, W.T. / Minogue, T.D. / Val, D.L. / Beck von Bodman, S. / Churchill, M.E.A.
Citation
Journal: Mol.Cell / Year: 2002
Title: Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing.
Authors: Watson, W.T. / Minogue, T.D. / Val, D.L. / von Bodman, S.B. / Churchill, M.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Rhenium MAD Phasing of the Acyl-homoserinelactone Synthase EsaI
Authors: Watson, W.T. / Murphy, F.V. / Gould, T.A. / Jambeck, P. / Val, D.L. / Cronan, J.E. / Beck von Bodman, S. / Churchill, M.E.A.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

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Assembly

Deposited unit
A: acyl-homoserinelactone synthase EsaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7928
Polymers26,0411
Non-polymers1,7517
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.390, 66.390, 47.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein acyl-homoserinelactone synthase EsaI


Mass: 26040.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pantoea stewartii subsp. stewartii (bacteria)
Species: Pantoea stewartii / Strain: subsp. stewartii / Gene: esaI/esaR cluster / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54656
#2: Chemical
ChemComp-REO / PERRHENATE / Perrhenate


Mass: 250.205 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: O4Re
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG 4000, 2-propanol, MES, EDTA, beta-mercaptoethanol, NaN3, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
20.1 MMES1reservoirpH6.1
314 %PEG40001reservoir
46 %isopropanol1reservoir
50.03 %beta-mercaptoethanol1reservoir
610 mMEDTA1reservoir
70.5 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.14, 1.1724, 1.1719, 1.19
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Nov 13, 1999 / Details: monochromator
RadiationMonochromator: parallel silicon crystal pair / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.141
21.17241
31.17191
41.191
ReflectionResolution: 2.5→30 Å / Num. all: 7168 / Num. obs: 7101 / % possible obs: 97 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 7.3 / Redundancy: 4.5 % / Biso Wilson estimate: 54.4 Å2 / Rsym value: 0.042 / Net I/σ(I): 20.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1373 / Rsym value: 0.175 / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 7283 / Num. measured all: 32922 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 98.1 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 4.7

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Processing

Software
NameVersionClassification
SOLVEphasing
RESOLVEmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(TRUNCATE)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 2.5→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 777 11 %RANDOM
Rwork0.216 ---
all0.222 7263 --
obs0.22 7101 97 %-
Displacement parametersBiso mean: 50.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2---0.9 Å20 Å2
3---1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 35 21 1571
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.98
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.038
RfactorNum. reflection% reflection
Rfree0.291 68 -
Rwork0.253 --
obs-719 98.7 %
Refinement
*PLUS
% reflection Rfree: 11 % / Rfactor all: 0.222 / Rfactor obs: 0.216 / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.253

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