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- PDB-3h77: Crystal structure of Pseudomonas aeruginosa PqsD in a covalent co... -

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Basic information

Entry
Database: PDB / ID: 3h77
TitleCrystal structure of Pseudomonas aeruginosa PqsD in a covalent complex with anthranilate
ComponentsPQS biosynthetic enzyme
KeywordsTRANSFERASE / PqsD / PQS / Anthraniloyl-CoA / Anthranilic acid / Anthranilate modified Cys
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-coenzyme A / Anthraniloyl-CoA anthraniloyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: PQS biosynthetic enzyme
B: PQS biosynthetic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5004
Polymers77,7272
Non-polymers1,7732
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-45.2 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.894, 59.656, 83.427
Angle α, β, γ (deg.)90.00, 103.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PQS biosynthetic enzyme


Mass: 38863.348 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: Chemical ChemComp-COW / Anthraniloyl-coenzyme A


Mass: 886.655 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H41N8O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1M Tris-HCl pH 8.5, 21% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 59980 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 6.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H76

3h76


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.161 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.335 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19488 3026 5 %RANDOM
Rwork0.15186 ---
obs0.15409 56914 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.632 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.06 Å2
2--0.16 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5160 0 114 582 5856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215387
X-RAY DIFFRACTIONr_angle_refined_deg1.6632.0097354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7965695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85123.75232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97315872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5611545
X-RAY DIFFRACTIONr_chiral_restr0.1420.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024108
X-RAY DIFFRACTIONr_nbd_refined0.2280.22813
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2522
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.230
X-RAY DIFFRACTIONr_mcbond_it1.151.53479
X-RAY DIFFRACTIONr_mcangle_it1.4625389
X-RAY DIFFRACTIONr_scbond_it3.07432153
X-RAY DIFFRACTIONr_scangle_it3.4014.51949
X-RAY DIFFRACTIONr_rigid_bond_restr2.89735632
X-RAY DIFFRACTIONr_sphericity_free4.5013598
X-RAY DIFFRACTIONr_sphericity_bonded2.8235274
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 197 -
Rwork0.172 4090 -
obs--97.79 %

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