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- PDB-2f3x: Crystal structure of FapR (in complex with effector)- a global re... -

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Basic information

Entry
Database: PDB / ID: 2f3x
TitleCrystal structure of FapR (in complex with effector)- a global regulator of fatty acid biosynthesis in B. subtilis
ComponentsTranscription factor fapR
KeywordsGENE REGULATION / 'hot-dog' fold - malonyl-CoA complex
Function / homology
Function and homology information


negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription factor FapR / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
MALONYL-COENZYME A / Transcription factor FapR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBuschiazzo, A. / Guerin, M.E. / Alzari, P.M.
CitationJournal: Embo J. / Year: 2006
Title: Structural basis of lipid biosynthesis regulation in Gram-positive bacteria.
Authors: Schujman, G.E. / Guerin, M. / Buschiazzo, A. / Schaeffer, F. / Llarrull, L.I. / Reh, G. / Vila, A.J. / Alzari, P.M. / de Mendoza, D.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN Nucleotidic portion of MLC could not be modeled due to lack of electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor fapR
B: Transcription factor fapR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2014
Polymers35,4942
Non-polymers1,7072
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-26 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.441, 89.441, 162.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly corresponds to the dimer in the ASU

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Components

#1: Protein Transcription factor fapR / Fatty acid and phospholipid biosynthesis regulator


Mass: 17746.998 Da / Num. of mol.: 2
Fragment: C-teminal domain + linker alpha helix (residues 44-188)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: fapR / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O34835
#2: Chemical ChemComp-MLC / MALONYL-COENZYME A / Malonyl-CoA


Mass: 853.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H38N7O19P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.8 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% ethylenglycol, 5mM malonyl-CoA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2004
RadiationMonochromator: Khozu monochromator with a McLennon controller containing a LN2 cooled Si111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.1→63.25 Å / Num. all: 12596 / Num. obs: 12596 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 19.3
Reflection shellResolution: 3.1→3.27 Å / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6 / Num. measured obs: 1780 / Num. unique all: 1780 / Rsym value: 0.31 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→63.25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 26.708 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.591 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 941 7.5 %RANDOM
Rwork0.187 ---
all0.19 12545 --
obs0.19 12545 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.544 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.69 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 3.1→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 64 10 2312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222320
X-RAY DIFFRACTIONr_bond_other_d0.0020.022177
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9913132
X-RAY DIFFRACTIONr_angle_other_deg0.94535045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.365284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8524.821112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.54215425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7491519
X-RAY DIFFRACTIONr_chiral_restr0.1070.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
X-RAY DIFFRACTIONr_nbd_refined0.2340.2471
X-RAY DIFFRACTIONr_nbd_other0.2060.22374
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21131
X-RAY DIFFRACTIONr_nbtor_other0.0980.21629
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.22
X-RAY DIFFRACTIONr_mcbond_it0.7931.51460
X-RAY DIFFRACTIONr_mcbond_other0.1171.5586
X-RAY DIFFRACTIONr_mcangle_it1.27522286
X-RAY DIFFRACTIONr_scbond_it1.9343937
X-RAY DIFFRACTIONr_scangle_it3.3424.5846
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 63 -
Rwork0.275 841 -
all-904 -
obs--100 %

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