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- PDB-4a0y: Structure of the global transcription regulator FapR from Staphyl... -

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Basic information

Entry
Database: PDB / ID: 4a0y
TitleStructure of the global transcription regulator FapR from Staphylococcus aureus
ComponentsTRANSCRIPTION FACTOR FAPR
KeywordsTRANSCRIPTION / LIPID HOMEOSTASIS
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 / metal ion 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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Roll ...Transcription factor FapR / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Transcription factor FapR
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAlbanesi, D. / Guerin, M.E. / Buschiazzo, A. / de Mendoza, D. / Alzari, P.M.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structural Basis for Feed-Forward Transcriptional Regulation of Membrane Lipid Homeostasis in Staphylococcus Aureus.
Authors: Albanesi, D. / Reh, G. / Guerin, M.E. / Schaeffer, F. / Debarbouille, M. / Buschiazzo, A. / Schujman, G.E. / De Mendoza, D. / Alzari, P.M.
History
DepositionSep 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)44,37211
Polymers44,0532
Non-polymers3199
Water93752
1
A: TRANSCRIPTION FACTOR FAPR
B: TRANSCRIPTION FACTOR FAPR
hetero molecules

A: TRANSCRIPTION FACTOR FAPR
B: TRANSCRIPTION FACTOR FAPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,74422
Polymers88,1054
Non-polymers63818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area9480 Å2
ΔGint-191.8 kcal/mol
Surface area28250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.520, 110.520, 115.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein TRANSCRIPTION FACTOR FAPR / FATTY ACID AND PHOSPHOLIPID BIOSYNTHESIS REGULATOR / REPRESSOR FACTOR FAPR


Mass: 22026.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: D6UB50, UniProt: Q2FZ56*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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 % / Description: NONE
Crystal growpH: 7.5 / Details: 3.5 M NACL, 0.1 MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→48 Å / Num. obs: 24146 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A0X

4a0x


Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.397 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21124 1293 5.1 %RANDOM
Rwork0.18522 ---
obs0.18651 24146 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.396 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 9 52 2492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222477
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9463343
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4424.492118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02815465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.611514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7191.51506
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51722455
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5533971
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3724.5888
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.597→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 98 -
Rwork0.31 1694 -
obs--96.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1413-0.3581-0.84893.05170.9998.1552-0.03410.1755-0.38410.0648-0.1607-0.05840.2575-0.01450.19470.2950.067-0.04760.301-0.03450.062471.406-57.119-17.829
21.4354-0.6443-0.34253.1760.32522.75740.00320.0897-0.1007-0.0289-0.040.30760.13380.00350.03670.21630.0253-0.01890.3256-0.06110.04162.314-35.5798.665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 68
2X-RAY DIFFRACTION2A69 - 189
3X-RAY DIFFRACTION2B69 - 189

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