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- PDB-2gfy: Structure of E. coli FabF(K335A) mutant with covalently linked do... -

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Basic information

Entry
Database: PDB / ID: 2gfy
TitleStructure of E. coli FabF(K335A) mutant with covalently linked dodecanoic acid
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / FabF / KASII / ketoacyl synthase
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 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSoisson, S.M. / Parthasarathy, G.
CitationJournal: Nature / Year: 2006
Title: Platensimycin is a selective FabF inhibitor with potent antibiotic properties.
Authors: Wang, J. / Soisson, S.M. / Young, K. / Shoop, W. / Kodali, S. / Galgoci, A. / Painter, R. / Parthasarathy, G. / Tang, Y.S. / Cummings, R. / Ha, S. / Dorso, K. / Motyl, M. / Jayasuriya, H. / ...Authors: Wang, J. / Soisson, S.M. / Young, K. / Shoop, W. / Kodali, S. / Galgoci, A. / Painter, R. / Parthasarathy, G. / Tang, Y.S. / Cummings, R. / Ha, S. / Dorso, K. / Motyl, M. / Jayasuriya, H. / Ondeyka, J. / Herath, K. / Zhang, C. / Hernandez, L. / Allocco, J. / Basilio, A. / Tormo, J.R. / Genilloud, O. / Vicente, F. / Pelaez, F. / Colwell, L. / Lee, S.H. / Michael, B. / Felcetto, T. / Gill, C. / Silver, L.L. / Hermes, J.D. / Bartizal, K. / Barrett, J. / Schmatz, D. / Becker, J.W. / Cully, D. / Singh, S.B.
History
DepositionMar 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7802
Polymers44,5791
Non-polymers2001
Water1,36976
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5594
Polymers89,1582
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area6950 Å2
ΔGint-47 kcal/mol
Surface area25420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.730, 74.730, 148.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological unit is a dimer. The second molecule of the dimer can be generated by the crystallographic symmetry operation

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2 / E.C.2.3.1.41 / 3-oxoacyl-[acyl-carrier-protein] synthase II / Beta-ketoacyl-ACP synthase II / KAS II / FabF


Mass: 44579.199 Da / Num. of mol.: 1 / Mutation: K335A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fabF, fabJ / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19-24% PEG 8000, 0.1M Tris, 10mM BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→64.6 Å / Num. all: 11514 / Num. obs: 11514 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 83.277 Å2 / Rsym value: 0.09
Reflection shellResolution: 2.85→3 Å / Rsym value: 0.423 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
MOLREPphasing
BUSTER-TNT1.3.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→64.55 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 553 4.8 %RANDOM
Rwork0.1656 ---
obs0.1691 11514 98.18 %-
Displacement parametersBiso mean: 55.31 Å2
Baniso -1Baniso -2Baniso -3
1--10.26769959 Å20 Å20 Å2
2---10.26769959 Å20 Å2
3---20.53539918 Å2
Refine analyzeLuzzati coordinate error obs: 0.3598 Å
Refinement stepCycle: LAST / Resolution: 2.85→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 13 76 3090
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01130652
X-RAY DIFFRACTIONt_angle_deg1.37241262
X-RAY DIFFRACTIONt_dihedral_angle_d24.5425890
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.013692
X-RAY DIFFRACTIONt_gen_planes0.0164635
X-RAY DIFFRACTIONt_it1.839305820
X-RAY DIFFRACTIONt_nbd0.079955
LS refinement shellResolution: 2.85→3.02 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2838 86 4.92 %
Rwork0.2114 1661 -
all21.5 1747 -
obs--98.18 %

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