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- PDB-5snq: PanDDA analysis group deposition -- Crystal Structure of Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 5snq
TitlePanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1891773476
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / FabF / beta-ketoacyl-acyl-carrier-protein synthase II
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
PHOSPHATE ION / Chem-Q5U / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.16 Å
AuthorsBrenk, R. / Georgiou, C.
Funding support Norway, 3items
OrganizationGrant numberCountry
Research Council of Norway273588 Norway
Research Council of Norway (RCN) through the NORCRYST245828 Norway
Research Council of Norway (RCN) through the NOR-OPENSCREEN245922 Norway
CitationJournal: Chemrxiv / Year: 2023
Title: PanDDA analysis group deposition
Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhinsky, V. / Haug, B.E. / Mainkar, P. / Brenk, R.
History
DepositionMay 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,11513
Polymers87,1382
Non-polymers97711
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-41 kcal/mol
Surface area25320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.112, 65.696, 84.352
Angle α, β, γ (deg.)90.000, 93.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 43569.000 Da / Num. of mol.: 2 / Mutation: C164Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fabF / Production host: Escherichia coli (E. coli)
References: UniProt: O54440, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-Q5U / 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-yl]-N-methylmethanamine


Mass: 179.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.19 Å3/Da / Density % sol: 43.88 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.20M ammonium formate, 26% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.16→47.9 Å / Num. obs: 40631 / % possible obs: 99.9 % / Redundancy: 3.3 % / CC1/2: 0.971 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.12 / Rrim(I) all: 0.22 / Net I/σ(I): 4.4 / Num. measured all: 133652 / Scaling rejects: 41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.16-2.223.41.0341003229670.5620.6581.2291.199.7
9.66-47.93.30.03916284860.9990.0240.04613.899

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: None

Resolution: 2.16→47.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.906 / SU B: 10.382 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.356 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 2020 5 %RANDOM
Rwork0.1932 ---
obs0.1967 38564 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.92 Å2 / Biso mean: 29.874 Å2 / Biso min: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å2-0 Å2-0.18 Å2
2---0.35 Å2-0 Å2
3----2.87 Å2
Refinement stepCycle: final / Resolution: 2.16→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 54 408 6536
Biso mean--61.03 35.58 -
Num. residues----824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137247
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156410
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.6379363
X-RAY DIFFRACTIONr_angle_other_deg1.3111.58214757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2425954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78120.826363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.499151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8071564
X-RAY DIFFRACTIONr_chiral_restr0.0660.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028406
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021666
X-RAY DIFFRACTIONr_mcbond_it1.9792.9683808
X-RAY DIFFRACTIONr_mcbond_other1.982.9683803
X-RAY DIFFRACTIONr_mcangle_it3.0094.4494642
LS refinement shellResolution: 2.158→2.214 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 121 -
Rwork0.321 2781 -
all-2902 -
obs--97.35 %

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