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- PDB-7tyb: Salicylate Adenylate PchD from Pseudomonas aeruginosa containing ... -

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Basic information

Entry
Database: PDB / ID: 7tyb
TitleSalicylate Adenylate PchD from Pseudomonas aeruginosa containing salicyl-AMS
ComponentsPyochelin biosynthesis protein PchD
KeywordsBIOSYNTHETIC PROTEIN / siderophore
Function / homology
Function and homology information


salicylate-[aryl-carrier protein] ligase / ligase activity / antibiotic biosynthetic process
Similarity search - Function
: / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
5'-O-[(2-hydroxybenzoyl)sulfamoyl]adenosine / Pyochelin synthase PchD
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsMeneely, K.M. / Shelton, C.L. / Lamb, A.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127655 United States
National Science Foundation (NSF, United States)1904494 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K12GM063651 United States
CitationJournal: J.Biol.Inorg.Chem. / Year: 2022
Title: Rational inhibitor design for Pseudomonas aeruginosa salicylate adenylation enzyme PchD.
Authors: Shelton, C.L. / Meneely, K.M. / Ronnebaum, T.A. / Chilton, A.S. / Riley, A.P. / Prisinzano, T.E. / Lamb, A.L.
History
DepositionFeb 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyochelin biosynthesis protein PchD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4492
Polymers59,9821
Non-polymers4661
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.064, 44.834, 67.199
Angle α, β, γ (deg.)90.000, 99.091, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Pyochelin biosynthesis protein PchD


Mass: 59982.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: pchD, PA4228 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q9HWG3
#2: Chemical ChemComp-KT0 / 5'-O-[(2-hydroxybenzoyl)sulfamoyl]adenosine


Mass: 466.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N6O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.2 M ammonium acetate, 0.1 M MES pH 5.4, 0.03 M ammonium chloride, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2016 / Details: Mirror: Rh coated flat bent mirror
RadiationMonochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.11→39.48 Å / Num. obs: 29938 / % possible obs: 99.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 17.06 Å2 / Rpim(I) all: 0.091 / Net I/σ(I): 7.5
Reflection shellResolution: 2.11→2.18 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2235 / Rpim(I) all: 0.426 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MDB

1mdb


Resolution: 2.11→37.01 Å / SU ML: 0.2384 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.5111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 1867 6.68 %
Rwork0.1677 26085 -
obs0.1717 27952 92.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.99 Å2
Refinement stepCycle: LAST / Resolution: 2.11→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4041 0 32 139 4212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01694200
X-RAY DIFFRACTIONf_angle_d1.64985710
X-RAY DIFFRACTIONf_chiral_restr0.0719628
X-RAY DIFFRACTIONf_plane_restr0.0145761
X-RAY DIFFRACTIONf_dihedral_angle_d8.3906602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.170.3191170.23171680X-RAY DIFFRACTION77.83
2.17-2.240.33211330.20141798X-RAY DIFFRACTION83.81
2.24-2.310.27521350.21441875X-RAY DIFFRACTION87.89
2.31-2.390.26221400.17551960X-RAY DIFFRACTION91.19
2.39-2.490.2851400.17331969X-RAY DIFFRACTION91.1
2.49-2.60.28911420.17481994X-RAY DIFFRACTION92.79
2.6-2.740.25221380.171994X-RAY DIFFRACTION93.39
2.74-2.910.2381470.17032029X-RAY DIFFRACTION93.71
2.91-3.130.23261500.16442080X-RAY DIFFRACTION96.04
3.13-3.450.20071530.15372119X-RAY DIFFRACTION97.8
3.45-3.950.16561550.1472153X-RAY DIFFRACTION98.84
3.95-4.970.17011550.13152183X-RAY DIFFRACTION99.11
4.97-37.010.22091620.18582251X-RAY DIFFRACTION99.46

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