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- PDB-6kvs: Staphylococcus aureus FabH with covalent inhibitor Oxa1 -

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Basic information

Entry
Database: PDB / ID: 6kvs
TitleStaphylococcus aureus FabH with covalent inhibitor Oxa1
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Covalent inhibitor / Complex / ketoacyl-ACP synthase III / ANTIBIOTIC / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 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-like
Similarity search - Domain/homology
Chem-OAX / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYuan, Y. / Wang, J.
CitationJournal: To Be Published
Title: Crystal Structure of S. aureus FabH, beta-ketoacyl carrier protein synthase
Authors: Qiu, X. / Choudhry, A.E.
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,3664
Polymers67,8332
Non-polymers5332
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-28 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.754, 91.573, 109.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 3 / ketoacyl-ACP synthase III / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP ...ketoacyl-ACP synthase III / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III


Mass: 33916.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu3 / ATCC 700698) (bacteria)
Strain: Mu3 / ATCC 700698 / Gene: fabH, SAHV_0978 / Production host: Escherichia coli (E. coli)
References: UniProt: A7X0K2, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-OAX / 4-chloranyl-N-[[cyclopropylmethyl(methanoyl)amino]methyl]benzamide


Mass: 266.723 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15ClN2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 4000 sodium citrate ammoinium acetate / PH range: 5.4-5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54056 Å
DetectorType: RIGAKU HyPic-6000HE / Detector: PIXEL / Date: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.3→22.4 Å / Num. obs: 29342 / % possible obs: 98.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.39
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.344 / Num. unique obs: 2936

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZOW

1zow


Resolution: 2.3→22.14 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.868 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.264 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 1471 5 %RANDOM
Rwork0.1984 ---
obs0.2016 27706 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.18 Å2 / Biso mean: 25.789 Å2 / Biso min: 9.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.3→22.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 0 261 5043
Biso mean---28.24 -
Num. residues----626
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 109 -
Rwork0.266 1991 -
all-2100 -
obs--98.31 %

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