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- PDB-3whb: Crystal structure of FadR from Bacillus subtilis, a transcription... -

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Basic information

Entry
Database: PDB / ID: 3whb
TitleCrystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation
ComponentsFatty acid metabolism regulator protein
KeywordsTRANSCRIPTION / transcriptional regulator / fatty acid degradation
Function / homology
Function and homology information


lipid catabolic process / fatty acid metabolic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Transcription regulator YsiA, C-terminal / YsiA-like protein, C-terminal region / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily ...Transcription regulator YsiA, C-terminal / YsiA-like protein, C-terminal region / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DODECYL-COA / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsFujihashi, M. / Nakatani, T. / Miki, K.
CitationJournal: Proteins / Year: 2014
Title: Structural characterization of a ligand-bound form of Bacillus subtilis FadR involved in the regulation of fatty acid degradation.
Authors: Fujihashi, M. / Nakatani, T. / Hirooka, K. / Matsuoka, H. / Fujita, Y. / Miki, K.
History
DepositionAug 23, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Fatty acid metabolism regulator protein
B: Fatty acid metabolism regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9653
Polymers44,0152
Non-polymers9501
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-43 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.167, 66.105, 99.029
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid metabolism regulator protein


Mass: 22007.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: fadR, ysiA, BSU28550 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P94548
#2: Chemical ChemComp-DCC / DODECYL-COA


Mass: 949.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H58N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.09 Å3/Da / Density % sol: 41.1 % / Mosaicity: 0.882 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 15%(w/v) polyetheleneglycol 4000, 300mM ammonium sulfate, pH 8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 20733 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.068 / Χ2: 1.035
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.2370.33320161.0721100
1.0691
1.0621
1.0811
1.0661
1.0181
1.0151
1.0371
0.9911
0.9481

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.15→49.56 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.244 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.945 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 1072 5.2 %RANDOM
Rwork0.2364 ---
obs0.2376 20614 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.33 Å2 / Biso mean: 41.0689 Å2 / Biso min: 23.09 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å20 Å20 Å2
2--4.35 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.15→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 61 37 3066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193083
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.9934155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2355378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.97525.882136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19815601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0311512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.2060.334830.2881395149598.863
2.206-2.2660.388800.3361348145598.144
2.266-2.3320.317740.2741337142798.879
2.332-2.4030.283620.2651317138199.855
2.403-2.4820.31790.2521272135799.558
2.482-2.5690.32590.2551232129299.923
2.569-2.6660.299520.27312051257100
2.666-2.7740.302740.25911501224100
2.774-2.8970.343450.27811101155100
2.897-3.0380.321540.2781058111399.91
3.038-3.2020.318510.27310211072100
3.202-3.3960.4430.2549651008100
3.396-3.6290.244490.225914963100
3.629-3.9190.196490.2839888100
3.919-4.290.163450.186788833100
4.29-4.7930.224520.166710762100
4.793-5.5280.225420.21630672100
5.528-6.7540.262390.261535574100
6.754-9.4820.159230.193447470100
9.482-55.710.181170.21326428598.596
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)
10.7898-0.13740.12520.9844-0.73370.96750.0888-0.017-0.1231-0.0396-0.01450.02340.08780.0688-0.07430.14260.0129-0.04050.0094-0.01120.141414.092836.68088.7456
20.8915-0.20880.48540.952-0.61071.48430.0709-0.221-0.0010.1935-0.0727-0.0101-0.1364-0.05290.00190.1588-0.0507-0.00320.0722-0.00290.099113.37852.982624.3874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 193
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B6 - 192

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