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- PDB-3ho2: Structure of E.coli FabF(C163A) in complex with Platencin -

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Basic information

Entry
Database: PDB / ID: 3ho2
TitleStructure of E.coli FabF(C163A) in complex with Platencin
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / FabF / platensimycin / platencin / ketoacyl synthase / Acyltransferase / Fatty acid biosynthesis / Lipid synthesis
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
Chem-N32 / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSoisson, S.M. / Parthasarathy, G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Isolation, enzyme-bound structure and antibacterial activity of platencin A1 from Streptomyces platensis.
Authors: Singh, S.B. / Ondeyka, J.G. / Herath, K.B. / Zhang, C. / Jayasuriya, H. / Zink, D.L. / Parthasarathy, G. / Becker, J.W. / Wang, J. / Soisson, S.M.
History
DepositionJun 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 13, 2021Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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
Revision 2.1Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,0312
Polymers44,6051
Non-polymers4251
Water9,062503
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)90,0614
Polymers89,2102
Non-polymers8512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area5770 Å2
ΔGint-53 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.148, 76.148, 145.299
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-697-

HOH

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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: 44605.238 Da / Num. of mol.: 1 / Mutation: C163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1095, fabF, fabJ, JW1081 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical ChemComp-N32 / 2,4-dihydroxy-3-({3-[(2S,4aS,8S,8aR)-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid / Platencin


Mass: 425.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27NO6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.88 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.04 Å / Num. all: 33760 / Num. obs: 33708 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 31.692 Å2 / Rsym value: 0.064 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 3308 / Rsym value: 0.423 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER-TNT2.5.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GFV
Resolution: 2→39.04 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1705 5.07 %RANDOM
Rwork0.1609 ---
obs0.1632 33656 99.62 %-
Displacement parametersBiso mean: 34.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.18662778 Å20 Å20 Å2
2---1.18662778 Å20 Å2
3---2.37325556 Å2
Refinement stepCycle: LAST / Resolution: 2→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 31 503 3538
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01130902
X-RAY DIFFRACTIONt_angle_deg1.57241712
X-RAY DIFFRACTIONt_dihedral_angle_d19.4735520
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.016772
X-RAY DIFFRACTIONt_gen_planes0.0194815
X-RAY DIFFRACTIONt_it1.738305620
X-RAY DIFFRACTIONt_nbd0.071695
LS refinement shellResolution: 2→2.12 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2524 268 5.07 %
Rwork0.1986 5018 -
all0.2012 5286 -
obs--99.62 %

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