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- PDB-9lpl: E. coli FabF mutant -C163Q -

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Basic information

Entry
Database: PDB / ID: 9lpl
TitleE. coli FabF mutant -C163Q
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / Complex / Inhibitor
Function / homology
Function and homology information


fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to cold / fatty acid biosynthetic process / protein homodimerization activity / cytosol
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
: / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, L. / Huang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82373772 China
CitationJournal: To Be Published
Title: Structure of E. coli FabF(C163Q) in complex with Platensimycin analog
Authors: Chen, L. / Huang, Y.
History
DepositionJan 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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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)94,3064
Polymers93,0992
Non-polymers1,2072
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-54 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.761, 79.761, 299.191
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2 / 3-oxoacyl-[acyl-carrier-protein] synthase II / Beta-ketoacyl-ACP synthase II / KAS II


Mass: 46549.414 Da / Num. of mol.: 2 / Mutation: C163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fabF, fabJ, b1095, JW1081 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical ChemComp-A1EWE / 3-(3-((2S,3S,5S,5aR,6S,12cR)-11-(tert-butyl)-2,6-dimethyl-7-oxo-1,2,3,4,5,5a,6,7-octahydro-2,5-epoxy-3,12c-methanobenzo[b]cyclohepta[5,6]benzo[1,2-d]thiophen-6-yl)propanamido)-2,4-dihydroxybenzoic acid


Mass: 603.725 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H37NO7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-Tris, 0.2 M Magnesium chloride, 20 % w/v polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 31093 / % possible obs: 98.61 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.06 / Rsym value: 0.188 / Net I/σ(I): 10.528
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.053 / Mean I/σ(I) obs: 1.811 / Num. unique obs: 4065 / Rpim(I) all: 0.334 / Rsym value: 1.053 / % possible all: 99.09

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→33.27 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.897 / SU B: 28.055 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.619 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26303 1503 4.8 %RANDOM
Rwork0.20384 ---
obs0.20668 29532 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.17 Å20 Å2
2--0.33 Å2-0 Å2
3----1.08 Å2
Refinement stepCycle: 1 / Resolution: 2.7→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5989 0 86 45 6120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0126191
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165831
X-RAY DIFFRACTIONr_angle_refined_deg2.9451.8128405
X-RAY DIFFRACTIONr_angle_other_deg0.9761.75113417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.645817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.441534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84410978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027397
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021365
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3443.8173274
X-RAY DIFFRACTIONr_mcbond_other5.3433.8173274
X-RAY DIFFRACTIONr_mcangle_it7.5786.8534089
X-RAY DIFFRACTIONr_mcangle_other7.5786.8534090
X-RAY DIFFRACTIONr_scbond_it6.4414.2462917
X-RAY DIFFRACTIONr_scbond_other6.444.2462918
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9687.6274317
X-RAY DIFFRACTIONr_long_range_B_refined10.66736.36916
X-RAY DIFFRACTIONr_long_range_B_other10.66636.36917
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.703→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 109 -
Rwork0.271 2163 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.933-0.0398-0.7011.0717-0.57582.6653-0.0085-0.13420.0488-0.0980.17350.1756-0.0526-0.2883-0.1650.0208-0.0228-0.01140.14160.04120.08085.3224-30.861834.7861
21.43150.4141-0.56361.1489-0.14972.1593-0.02470.05140.1423-0.21440.1336-0.0206-0.24910.1633-0.10880.1488-0.10290.0340.0843-0.01010.081225.0315-21.107215.6013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 411
2X-RAY DIFFRACTION2B2 - 411

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