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- PDB-1ro5: Crystal Structure of the AHL Synthase LasI -

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Basic information

Entry
Database: PDB / ID: 1ro5
TitleCrystal Structure of the AHL Synthase LasI
ComponentsAutoinducer synthesis protein lasI
KeywordsSIGNALING PROTEIN / alpha-beta-alpha sandwich / phosphopantetheine fold
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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsGould, T.A. / Schweizer, H.P. / Churchill, M.E.
CitationJournal: Mol.Microbiol. / Year: 2004
Title: Structure of the Pseudomonas aeruginosa acyl-homoserinelactone synthase LasI.
Authors: Gould, T.A. / Schweizer, H.P. / Churchill, M.E.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autoinducer synthesis protein lasI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1106
Polymers22,6601
Non-polymers4505
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Autoinducer synthesis protein lasI
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)277,31972
Polymers271,92312
Non-polymers5,39660
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation16_544x,-y-1/2,-z-1/21
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation27_554-x+1/2,y,-z-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
crystal symmetry operation33_554y+1/2,z,x-1/21
crystal symmetry operation38_545-x+1/2,-y-1/2,z1
crystal symmetry operation41_545z+1/2,x-1/2,y1
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
Buried area31610 Å2
ΔGint-921 kcal/mol
Surface area95210 Å2
MethodPISA, PQS
3
A: Autoinducer synthesis protein lasI
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)277,31972
Polymers271,92312
Non-polymers5,39660
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation33_554y+1/2,z,x-1/21
crystal symmetry operation34_555-y+1/2,z,-x+1/21
crystal symmetry operation35_555y+1/2,-z,-x+1/21
crystal symmetry operation36_554-y+1/2,-z,x-1/21
crystal symmetry operation41_545z+1/2,x-1/2,y1
crystal symmetry operation42_555z+1/2,-x+1/2,-y1
crystal symmetry operation43_555-z+1/2,-x+1/2,y1
crystal symmetry operation44_545-z+1/2,x-1/2,-y1
Buried area26280 Å2
ΔGint-773 kcal/mol
Surface area100540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.900, 154.900, 154.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-402-

SO4

21A-403-

SO4

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Components

#1: Protein Autoinducer synthesis protein lasI / AHL SYNTHASE LASI


Mass: 22660.248 Da / Num. of mol.: 1
Mutation: Deletion of residues 60, 61, 62, 63, and insertion of 60G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: LASI, PA1432 / Plasmid: pViet / Production host: Escherichia coli (E. coli) / Strain (production host): SA1503 (DE3) / References: UniProt: P33883
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Ammonium Sulfate, Sodium Sulfate, MOPS, NaCl, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 11, 2001 / Details: Undulator A
RadiationMonochromator: SI 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→500 Å / Num. obs: 13180 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.52 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 25.14
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 4 / Num. unique all: 1067 / % possible all: 77

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→35.58 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.543 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.208
Details: CNS was also used in refinement. Only the S for SO4 402 and 403 is present in the coordinates.
RfactorNum. reflection% reflectionSelection details
Rfree0.23637 1338 9.9 %RANDOM
Rwork0.19251 ---
all0.1971 13860 --
obs0.19712 12210 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.441 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 13 58 1632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0211625
X-RAY DIFFRACTIONr_angle_refined_deg2.3821.9672191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6715195
X-RAY DIFFRACTIONr_chiral_restr0.1880.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021195
X-RAY DIFFRACTIONr_nbd_refined0.260.2706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.283
X-RAY DIFFRACTIONr_metal_ion_refined0.1660.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.7330.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3120.29
X-RAY DIFFRACTIONr_mcbond_it1.7281.5973
X-RAY DIFFRACTIONr_mcangle_it3.15121564
X-RAY DIFFRACTIONr_scbond_it4.8983652
X-RAY DIFFRACTIONr_scangle_it7.6914.5627
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.327 80
Rwork0.23 877

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