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- PDB-3il5: Structure of E. faecalis FabH in complex with 2-({4-bromo-3-[(die... -

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Basic information

Entry
Database: PDB / ID: 3il5
TitleStructure of E. faecalis FabH in complex with 2-({4-bromo-3-[(diethylamino)sulfonyl]benzoyl}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-B82 / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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


Theoretical massNumber of molelcules
Total (without water)152,4758
Polymers150,6544
Non-polymers1,8214
Water2,306128
1
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)76,2384
Polymers75,3272
Non-polymers9112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-45 kcal/mol
Surface area21920 Å2
MethodPISA
2
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2384
Polymers75,3272
Non-polymers9112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-44 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.586, 84.973, 114.390
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number4
Space group name H-MP1211

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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: 37663.496 Da / Num. of mol.: 4
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-B82 / 2-({[4-bromo-3-(diethylsulfamoyl)phenyl]carbonyl}amino)benzoic acid / 2-({4-bromo-3-[(diethylamino)sulfonyl]benzoyl}amino)benzoic acid


Mass: 455.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19BrN2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350, 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: 2.6→25 Å / Num. all: 38916 / Num. obs: 38358 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 11.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3767 / Rsym value: 0.338 / % possible all: 97.3

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Processing

Software
NameClassification
MAR345dtbdata collection
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IL9

3il9


Resolution: 2.6→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 3691 -Random
Rwork0.1891 ---
all0.191 38916 --
obs-38358 94.4 %-
Displacement parametersBiso max: 123.34 Å2 / Biso mean: 43.762 Å2 / Biso min: 12.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.099 Å20 Å20.033 Å2
2---0.594 Å20 Å2
3---0.495 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9838 0 108 128 10074
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.2161.5
X-RAY DIFFRACTIONc_scbond_it1.8782
X-RAY DIFFRACTIONc_mcangle_it2.0392
X-RAY DIFFRACTIONc_scangle_it2.8092.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.387 580 -
Rwork0.305 --
obs-5470 86.1 %

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