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- PDB-7tz4: Salicylate Adenylate PchD from Pseudomonas aeruginosa containing ... -

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Basic information

Entry
Database: PDB / ID: 7tz4
TitleSalicylate Adenylate PchD from Pseudomonas aeruginosa containing 4-cyanosalicyl-AMS
ComponentsPyochelin biosynthesis salicyl-AMP ligase PchD
KeywordsBIOSYNTHETIC PROTEIN / adenylate syntase / salicylate
Function / homology
Function and homology information


ligase activity / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
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
Chem-KUX / (2,3-dihydroxybenzoyl)adenylate synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsShelton, C.L. / Meneely, K.M. / 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 15, 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 salicyl-AMP ligase PchD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4742
Polymers59,9821
Non-polymers4911
Water5,260292
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)177.060, 44.854, 66.615
Angle α, β, γ (deg.)90.000, 99.180, 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 salicyl-AMP ligase PchD


Mass: 59982.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pchD, LYSZa2_15910, LYSZa5_15910 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8A4FQG3, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-KUX / 5'-O-[(4-cyano-2-hydroxybenzoyl)sulfamoyl]adenosine


Mass: 491.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17N7O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M MES pH 5.6, 0.03 M ammonium chloride, 26% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.69→36.93 Å / Num. obs: 56335 / % possible obs: 97.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.56 Å2 / Rpim(I) all: 0.062 / Net I/σ(I): 8.6
Reflection shellResolution: 1.69→1.72 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2309 / Rpim(I) all: 0.526

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TYB

7tyb


Resolution: 1.69→36.93 Å / SU ML: 0.1525 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3318
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1786 1999 3.55 %
Rwork0.1512 54239 -
obs0.1522 56238 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.7 Å2
Refinement stepCycle: LAST / Resolution: 1.69→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 34 292 4417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114240
X-RAY DIFFRACTIONf_angle_d1.06295762
X-RAY DIFFRACTIONf_chiral_restr0.1966632
X-RAY DIFFRACTIONf_plane_restr0.0075769
X-RAY DIFFRACTIONf_dihedral_angle_d13.8711589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.740.28531230.23423347X-RAY DIFFRACTION84.02
1.74-1.780.22781410.1983819X-RAY DIFFRACTION96.66
1.78-1.840.22281430.17363912X-RAY DIFFRACTION99.17
1.84-1.890.19841450.16073935X-RAY DIFFRACTION99.05
1.89-1.960.19821440.15833877X-RAY DIFFRACTION98.03
1.96-2.040.1861430.14893901X-RAY DIFFRACTION98.3
2.04-2.130.18251440.14333895X-RAY DIFFRACTION97.77
2.13-2.250.18381400.13283800X-RAY DIFFRACTION96.47
2.25-2.390.16861450.13463946X-RAY DIFFRACTION99.27
2.39-2.570.17911460.14043942X-RAY DIFFRACTION99.22
2.57-2.830.15881450.14243942X-RAY DIFFRACTION98.43
2.83-3.240.17951420.14823856X-RAY DIFFRACTION96.38
3.24-4.080.15781490.14424027X-RAY DIFFRACTION99.55
4.08-36.930.16281490.15654040X-RAY DIFFRACTION97.65

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