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

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Basic information

Entry
Database: PDB / ID: 5sno
TitlePanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z364368134
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. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
PHOSPHATE ION / 3-acetamido-2-methylbenzoic acid / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.86 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

Downloads & links

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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)88,49616
Polymers87,1382
Non-polymers1,35814
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-48 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.852, 65.844, 83.867
Angle α, β, γ (deg.)90.000, 103.760, 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-Q5H / 3-acetamido-2-methylbenzoic acid


Mass: 193.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.08 Å3/Da / Density % sol: 40.73 % / 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: 1.86→58.86 Å / Num. obs: 60012 / % possible obs: 99.8 % / Redundancy: 3.2 % / CC1/2: 0.98 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.117 / Rrim(I) all: 0.214 / Net I/σ(I): 4.1 / Num. measured all: 191567 / Scaling rejects: 110
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
1.86-1.912.71.0061200744250.3670.7481.2591.199.6
8.32-58.863.20.0522737110.9950.0330.069.899.8

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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: 1.86→58.9 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.129 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 2956 4.9 %RANDOM
Rwork0.224 ---
obs0.2257 57029 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.51 Å2 / Biso mean: 19.884 Å2 / Biso min: 7.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å2-0 Å20.87 Å2
2---1.21 Å2-0 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 1.86→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 78 25 6177
Biso mean--36.24 18.67 -
Num. residues----824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137347
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156422
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.6439412
X-RAY DIFFRACTIONr_angle_other_deg1.3321.58514771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2825954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31120.826363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.852151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2841564
X-RAY DIFFRACTIONr_chiral_restr0.0680.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028570
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021678
X-RAY DIFFRACTIONr_mcbond_it1.1471.9623843
X-RAY DIFFRACTIONr_mcbond_other1.1511.9633819
X-RAY DIFFRACTIONr_mcangle_it1.8212.9374654
LS refinement shellResolution: 1.858→1.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 230 -
Rwork0.334 4068 -
all-4298 -
obs--96.41 %

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