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- PDB-3il6: Structure of E. faecalis FabH in complex with 2-({4-[(3R,5S)-3,5-... -

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Basic information

Entry
Database: PDB / ID: 3il6
TitleStructure of E. faecalis FabH in complex with 2-({4-[(3R,5S)-3,5-dimethylpiperidin-1-yl]-3-phenoxybenzoyl}amino)benzoic acid
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / FabH / fatty acid biosynthesis / antibiotic / Acyltransferase / Cytoplasm / Lipid synthesis / Multifunctional enzyme
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/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-B83 / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGajiwala, K.S. / Margosiak, S. / Lu, J. / Cortez, J. / Su, Y. / Nie, Z. / Appelt, K.
CitationJournal: Febs Lett. / Year: 2009
Title: Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme.
Authors: Gajiwala, K.S. / Margosiak, S. / Lu, J. / Cortez, J. / Su, Y. / Nie, Z. / Appelt, K.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2078
Polymers35,1861
Non-polymers1,0217
Water2,018112
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)72,41416
Polymers70,3722
Non-polymers2,04214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_378y-2,x+2,-z+31
Buried area6170 Å2
ΔGint-49 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.263, 119.263, 68.921
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 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III


Mass: 35185.875 Da / Num. of mol.: 1 / Mutation: D36A, E37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EF_2885, fabH / Production host: Escherichia coli (E. coli)
References: UniProt: Q820T1, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-B83 / 2-[({4-[(3R,5S)-3,5-dimethylpiperidin-1-yl]-3-phenoxyphenyl}carbonyl)amino]benzoic acid / 2-({4-[(3R,5S)-3,5-dimethylpiperidin-1-yl]-3-phenoxybenzoyl}amino)benzoic acid


Mass: 444.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N2O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
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: 4.02 Å3/Da / Density % sol: 69.41 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 20488 / Num. obs: 19811 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 21.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.33 / Num. unique all: 1939 / Rsym value: 0.361 / % possible all: 99.5

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Processing

Software
NameClassification
MAR345dtbdata collection
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IL5

3il5


Resolution: 2.5→24.36 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 519487.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1874 9.8 %RANDOM
Rwork0.185 ---
all0.19 20488 --
obs0.19 19129 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.9522 Å2 / ksol: 0.355255 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1--8.12 Å20.89 Å20 Å2
2---8.12 Å20 Å2
3---16.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 63 112 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 285 9.5 %
Rwork0.229 2713 -
obs-1939 91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION32059.param
X-RAY DIFFRACTION4so4.param
X-RAY DIFFRACTION5cis_peptide.param

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