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- PDB-3h76: Crystal structure of PqsD, a key enzyme in Pseudomonas aeruginosa... -

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Basic information

Entry
Database: PDB / ID: 3h76
TitleCrystal structure of PqsD, a key enzyme in Pseudomonas aeruginosa quinolone signal biosynthesis pathway
ComponentsPQS biosynthetic enzyme
KeywordsTRANSFERASE / PqsD / PQS / ANTHRANILOYL-CoA / ANTHRANILIC ACID
Function / homology
Function and homology information


anthraniloyl-CoA anthraniloyltransferase / secondary metabolite biosynthetic process / acyltransferase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Anthraniloyl-CoA anthraniloyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBera, A.K. / Atanasova, V. / Parsons, J.F.
CitationJournal: Biochemistry / Year: 2009
Title: Structure of PqsD, a Pseudomonas quinolone signal biosynthetic enzyme, in complex with anthranilate.
Authors: Bera, A.K. / Atanasova, V. / Robinson, H. / Eisenstein, E. / Coleman, J.P. / Pesci, E.C. / Parsons, J.F.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: PQS biosynthetic enzyme
B: PQS biosynthetic enzyme


Theoretical massNumber of molelcules
Total (without water)77,4882
Polymers77,4882
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-44.1 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.081, 90.420, 67.894
Angle α, β, γ (deg.)90.00, 95.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PQS biosynthetic enzyme


Mass: 38744.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PA01 / 1C / PRS 101 / LMG 12228 / Gene: pqsD, PA0999 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P20582, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 1.94 Å3/Da / Density % sol: 36.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.16 M MgCl2, 0.08M Tris-HCl pH 8.5, 24% PEG 4000, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→27 Å / Num. obs: 49952 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 5.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.07 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.6 / % possible all: 88.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HN9

1hn9


Resolution: 1.8→25.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.617 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26593 2528 5.1 %RANDOM
Rwork0.19822 ---
obs0.20167 47404 91.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.725 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0.18 Å2
2---0.12 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 0 0 348 5355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0215126
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9796978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4015673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46723.378225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9715846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0421547
X-RAY DIFFRACTIONr_chiral_restr0.1280.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023911
X-RAY DIFFRACTIONr_nbd_refined0.2410.22609
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2590.2355
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.217
X-RAY DIFFRACTIONr_mcbond_it1.3121.53394
X-RAY DIFFRACTIONr_mcangle_it1.92625273
X-RAY DIFFRACTIONr_scbond_it3.0331922
X-RAY DIFFRACTIONr_scangle_it4.2364.51696
X-RAY DIFFRACTIONr_rigid_bond_restr2.03135316
X-RAY DIFFRACTIONr_sphericity_free9.1563393
X-RAY DIFFRACTIONr_sphericity_bonded4.38235027
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 183 -
Rwork0.304 3330 -
obs--88.31 %

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