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- PDB-3g11: Structure of E. coli FabF(C163Q) in complex with dihydrophenyl pl... -

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Basic information

Entry
Database: PDB / ID: 3g11
TitleStructure of E. coli FabF(C163Q) in complex with dihydrophenyl platensimycin
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / ketoacyl synthase / 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
Chem-P9C / 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 Å
AuthorsSoisson, S.M. / Parthasarathy, G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Synthesis and biological evaluation of platensimycin analogs.
Authors: Shen, H.C. / Ding, F.X. / Singh, S.B. / Parthasarathy, G. / Soisson, S.M. / Ha, S.N. / Chen, X. / Kodali, S. / Wang, J. / Dorso, K. / Tata, J.R. / Hammond, M.L. / Maccoss, M. / Colletti, S.L.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Oct 20, 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:
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)45,1822
Polymers44,6621
Non-polymers5201
Water7,278404
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)90,3644
Polymers89,3252
Non-polymers1,0392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area5720 Å2
ΔGint-53 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.283, 76.283, 146.579
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-417-

HOH

21A-551-

HOH

31A-702-

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: 44662.289 Da / Num. of mol.: 1 / Mutation: C163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b1095, fabF, fabJ, JW1081 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical ChemComp-P9C / 3-({3-[(1S,4S,4aS,6S,7S,9S,9aR)-1,6-dimethyl-2-oxo-4-phenyldecahydro-6,9-epoxy-4a,7-methanobenzo[7]annulen-1-yl]propanoyl}amino)-2,4-dihydroxybenzoic acid


Mass: 519.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H33NO7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→66 Å / Num. obs: 34015 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.041 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 36.572
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.471 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
TNTrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
BUSTER-TNT2.1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GFX

2gfx


Resolution: 2→65.94 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 1720 5.06 %RANDOM
Rwork0.166 ---
obs0.168 33972 99.59 %-
all-34057 --
Displacement parametersBiso mean: 34.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.6918442 Å20 Å20 Å2
2---2.6918442 Å20 Å2
3---5.3836884 Å2
Refinement stepCycle: LAST / Resolution: 2→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 38 404 3450
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01131032
X-RAY DIFFRACTIONt_angle_deg1.38641922
X-RAY DIFFRACTIONt_dihedral_angle_d18.6465540
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.003788
X-RAY DIFFRACTIONt_gen_planes0.0144718
X-RAY DIFFRACTIONt_it1.764310320
X-RAY DIFFRACTIONt_nbd0.134625
LS refinement shellResolution: 2→2.12 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2381 265 4.96 %
Rwork0.2143 5076 -
all0.2155 5341 -
obs--99.59 %

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