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- PDB-3i8p: Crystal structure of E. coli FabF(C163A) in complex with Platensi... -

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Basic information

Entry
Database: PDB / ID: 3i8p
TitleCrystal structure of E. coli FabF(C163A) in complex with Platensimycin A1
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / FabF / KASII / platensimycin A1 / platensimycin / 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 A1 / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSoisson, S.M. / Parthsarathy, 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
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 1.4Sep 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:
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)45,0612
Polymers44,6051
Non-polymers4551
Water9,692538
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)90,1214
Polymers89,2102
Non-polymers9112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area5880 Å2
ΔGint-56.6 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.016, 76.016, 144.941
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-413-

HOH

21A-515-

HOH

31A-723-

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: fabF, fabJ, b1095, JW1081 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical ChemComp-840 / Platensimycin A1 / 2,4-dihydroxy-3-({3-[(1aR,2R,3R,3aS,7S,7aS,7bR)-3-hydroxy-2,7-dimethyl-6-oxo-2,3,7,7a-tetrahydro-6H-2,7b-epoxy-1a,3a-me thanocyclopropa[a]naphthalen-7(1H)-yl]propanoyl}amino)benzoic acid


Mass: 455.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25NO8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19-24% PEG 8000, 0.1M Tris-HCl, 10mM BME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 40801 / Num. obs: 38907 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.089 / Χ2: 1.385 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.977.20.47938040.9711100
1.97-2.057.20.33638551.0351100
2.05-2.147.30.26538021.2451100
2.14-2.257.20.20738531.4021100
2.25-2.397.30.17238491.5431100
2.39-2.587.30.13838771.4731100
2.58-2.847.20.10938831.6361100
2.84-3.257.10.08639021.6951100
3.25-4.096.90.06339541.4811100
4.09-506.70.04841281.359199.6

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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
BUSTER-TNT2.1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GFW

2gfw


Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1949 5.02 %RANDOM
Rwork0.157 ---
obs0.158 38907 99.53 %-
all-38907 --
Displacement parametersBiso max: 127.24 Å2 / Biso mean: 28.637 Å2 / Biso min: 5.71 Å2
Baniso -1Baniso -2Baniso -3
1--3.028 Å20 Å20 Å2
2---3.028 Å20 Å2
3---6.055 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 33 538 3575
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01130932
X-RAY DIFFRACTIONt_angle_deg1.72441792
X-RAY DIFFRACTIONt_dihedral_angle_d18.9435520
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.004768
X-RAY DIFFRACTIONt_gen_planes0.0154838
X-RAY DIFFRACTIONt_it1.606305620
X-RAY DIFFRACTIONt_nbd0.182655
LS refinement shellResolution: 1.9→2.01 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.235 292 4.81 %
Rwork0.199 5773 -
all0.201 6065 -
obs--99.53 %

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