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- PDB-3hnz: Structure of E. coli FabF(C163A) in Complex with Platensimycin -

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Basic information

Entry
Database: PDB / ID: 3hnz
TitleStructure of E. coli FabF(C163A) in Complex with Platensimycin
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / Platensimycin analog / FabF / 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
PLATENSIMYCIN / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 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 1.2Nov 1, 2017Group: Refinement description / Category: software
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 2.1Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)45,0472
Polymers44,6051
Non-polymers4411
Water1,72996
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)90,0934
Polymers89,2102
Non-polymers8832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area7470 Å2
ΔGint-71 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.665, 74.665, 146.274
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-424-

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: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical ChemComp-PMN / PLATENSIMYCIN / Platensimycin


Mass: 441.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27NO7 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.64 Å3/Da / Density % sol: 53.39 %

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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 / Date: Jul 14, 2004
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→38.93 Å / Num. obs: 12790 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Χ2: 1.249 / Net I/σ(I): 18.917
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.75-2.853.50.41912280.95100
2.85-2.963.50.31412701.078100
2.96-3.13.60.24112681.15100
3.1-3.263.60.15612551.248100
3.26-3.463.50.12412461.445100
3.46-3.733.50.08812851.41799.9
3.73-4.113.40.06812621.40499.9
4.11-4.73.40.04613011.19799.9
4.7-5.923.40.04212981.35199.8
5.92-503.20.02813771.25798.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
TNTrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNT2.5.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→38.93 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 623 4.89 %RANDOM
Rwork0.178 ---
obs0.182 -99.55 %-
Displacement parametersBiso max: 170.62 Å2 / Biso mean: 53.665 Å2 / Biso min: 24.69 Å2
Baniso -1Baniso -2Baniso -3
1--6.802 Å20 Å20 Å2
2---6.802 Å20 Å2
3---13.603 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 32 96 3132
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01130922
X-RAY DIFFRACTIONt_angle_deg1.43141772
X-RAY DIFFRACTIONt_dihedral_angle_d25.0915830
X-RAY DIFFRACTIONIMPROPER ANGLES (DEGREES)4.80260
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.003768
X-RAY DIFFRACTIONt_gen_planes0.0114808
X-RAY DIFFRACTIONt_it1.551309220
X-RAY DIFFRACTIONt_nbd0.121935
LS refinement shellResolution: 2.75→2.92 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.394 111 5.59 %
Rwork0.253 1876 -
all0.261 1987 -
obs--99.55 %

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