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- PDB-3whc: Crystal structure of a transcriptional regulator FadR from Bacill... -

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Basic information

Entry
Database: PDB / ID: 3whc
TitleCrystal structure of a transcriptional regulator FadR from Bacillus subtilis in complex with stearoyl-CoA
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
STEAROYL-COENZYME A / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Fatty acid metabolism regulator protein
B: Fatty acid metabolism regulator protein
C: Fatty acid metabolism regulator protein
D: Fatty acid metabolism regulator protein
E: Fatty acid metabolism regulator protein
F: Fatty acid metabolism regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,24912
Polymers132,0456
Non-polymers6,2046
Water2,072115
1
A: Fatty acid metabolism regulator protein
B: Fatty acid metabolism regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0834
Polymers44,0152
Non-polymers2,0682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-32 kcal/mol
Surface area16320 Å2
MethodPISA
2
C: Fatty acid metabolism regulator protein
D: Fatty acid metabolism regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0834
Polymers44,0152
Non-polymers2,0682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-30 kcal/mol
Surface area16090 Å2
MethodPISA
3
E: Fatty acid metabolism regulator protein
F: Fatty acid metabolism regulator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0834
Polymers44,0152
Non-polymers2,0682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-35 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.305, 88.762, 199.952
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.: 6
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-ST9 / STEAROYL-COENZYME A


Mass: 1033.996 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H70N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 25%(w/v) polyethyleneglycol 3350, 200mM lithium sulfate, 100mM Tris-Cl (pH 9) , VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / 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: 2.2→50.04 Å / Num. obs: 61396 / % possible obs: 95.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 21.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.256 / % possible all: 86.9

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WHB

3whb


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.51 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.361 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 3105 5.1 %RANDOM
Rwork0.2386 ---
obs0.2403 61322 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.34 Å2 / Biso mean: 35.8671 Å2 / Biso min: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.43 Å20 Å2-0 Å2
2--0.08 Å20 Å2
3----3.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8774 0 402 115 9291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0199286
X-RAY DIFFRACTIONr_angle_refined_deg0.9632.01812535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.57651126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5825.838382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.162151693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6321533
X-RAY DIFFRACTIONr_chiral_restr0.0550.21472
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026527
LS refinement shellResolution: 2.198→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 193 -
Rwork0.298 3844 -
all-4037 -
obs--85.64 %
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)
13.08420.74111.17962.4384-0.95468.10810.0970.0445-0.222-0.202-0.1178-0.04240.8786-0.08350.02090.2048-0.02350.0160.1264-0.040.1978-8.11583.8316-60.2119
21.35770.27060.18942.61450.27193.4016-0.11580.04530.21570.13780.033-0.2261-0.24540.12050.08270.04030.007-0.03710.12650.02180.237-3.021716.6518-41.7869
34.3773-0.53820.60142.24130.45993.7928-0.2758-0.18950.31020.22760.2094-0.1173-0.43250.0790.06640.09330.0343-0.02880.07120.01360.1632-2.153911.8642-30.1291
416.65986.49397.70988.86230.09594.9757-0.547-0.17620.1221-0.15870.2717-0.5973-0.3797-0.13490.27530.1952-0.08460.09930.2708-0.0820.30668.239913.683-42.6412
54.35060.0759-1.46588.03540.70263.76170.13950.043-0.22570.0820.0144-0.52350.16490.1506-0.15390.0266-0.0070.00230.09-0.00580.272915.9782-15.9206-44.1733
61.2591-1.0554-1.40092.05441.57784.6496-0.0871-0.2666-0.08370.32210.1618-0.23630.24510.1756-0.07460.06690.0154-0.03650.12410.0120.29829.5181-1.6855-26.9539
73.44820.5732-1.27842.8943-1.09984.9567-0.1307-0.14970.24230.25490.1291-0.2836-0.35360.04420.00160.06270.019-0.07890.0618-0.03950.26888.202410.4753-28.8499
82.0493-2.6644-1.97055.49830.29954.6372-0.3244-0.3815-0.04140.63080.48770.18680.06360.1251-0.16320.10320.05460.00940.34160.02930.2015-1.6159-2.3667-30.307
94.72781.2865-0.73463.0966-1.05879.64740.00590.16280.09730.1589-0.04190.0924-0.3599-0.16210.03590.02290.0178-0.01750.1810.00310.2143-26.5383-0.756-28.3331
101.37440.7633-0.09643.2334-2.15414.72650.0210.1481-0.2403-0.1745-0.0771-0.02830.6974-0.05710.05620.19490.0019-0.01280.1707-0.05640.2571-27.4214-13.7999-9.1921
112.0783-0.547-0.06753.1108-0.98264.62380.0375-0.0507-0.16310.1752-0.0935-0.01390.3780.11210.0560.07290.0341-0.01110.0976-0.01220.2043-24.5776-9.56282.0366
125.6709-3.666-0.33844.34714.35238.9888-0.0261-0.3815-0.49950.2248-0.01090.33730.7557-0.56070.0370.3178-0.0605-0.0450.2509-0.01860.2865-38.0295-10.4176-6.7911
134.70731.02941.74418.0142-1.14651.01730.03170.15890.1936-0.23790.03010.6143-0.016-0.0883-0.06180.18130.1193-0.03740.33180.03740.3646-43.475119.8228-5.4753
141.6056-1.0321.97482.6298-2.41383.4791-0.097-0.18170.10270.29260.13910.1289-0.4563-0.2188-0.04210.16150.01060.0140.1657-0.02020.2738-33.9374.54638.5955
153.67810.54581.0792.6076-0.25744.58020.0058-0.088-0.0940.19820.04970.11180.2279-0.2491-0.05550.1-0.01140.02740.1067-0.01480.2211-34.2401-7.586.3055
160.8937-1.9177-1.888.17710.89426.5212-0.0398-0.11140.05960.3416-0.0703-0.4937-0.39410.50480.11010.3492-0.0508-0.02920.1081-0.01090.2532-24.39184.33922.3578
173.3233-0.5424-0.3950.6341.10876.28730.27820.0671-0.3763-0.0826-0.18290.03110.53530.0299-0.09530.1973-0.0244-0.07520.2150.01150.27032.8591.03934.5309
180.90120.77590.00182.93540.42594.5055-0.0049-0.04950.1379-0.04090.15710.1197-0.2736-0.4222-0.15220.0623-0.0097-0.00290.25670.06660.2429-0.759613.029823.7979
193.0043-0.11280.09942.52710.63754.30280.0149-0.05780.07890.1350.09230.1728-0.0032-0.684-0.10720.0608-0.0648-0.02760.3030.10020.1963-4.55567.721434.1626
204.9105-0.81174.87774.87542.56938.36330.1324-0.10280.1440.41080.117-0.29920.0889-0.0852-0.24940.2293-0.03690.05080.1750.04350.21349.82210.566827.3554
216.80331.81621.144713.3438-0.06691.34050.12010.1383-0.0155-2.16070.2353-2.01880.17960.6868-0.35540.9792-0.14980.44670.4665-0.24480.803817.9077-19.030828.2757
223.1799-1.8635-1.32044.68291.99013.483-0.2898-0.0221-0.3738-0.12650.19270.00851.024-0.26040.09710.4549-0.15870.03090.14490.0350.24055.1852-5.454141.7126
234.89390.6591-1.08942.0315-0.87656.5087-0.1188-0.02190.0078-0.17110.20690.10070.2449-0.6489-0.08810.0337-0.0437-0.04280.09040.03050.17294.82446.594939.6192
242.866-5.69232.392111.826-4.21322.5906-0.17010.0555-0.17180.437-0.08530.69860.018-0.04390.25540.3334-0.13680.05230.43610.00040.3938-3.0973-6.151934.2219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 57
2X-RAY DIFFRACTION2A58 - 143
3X-RAY DIFFRACTION3A144 - 193
4X-RAY DIFFRACTION4A201
5X-RAY DIFFRACTION5B6 - 57
6X-RAY DIFFRACTION6B58 - 143
7X-RAY DIFFRACTION7B144 - 193
8X-RAY DIFFRACTION8B201
9X-RAY DIFFRACTION9C5 - 57
10X-RAY DIFFRACTION10C58 - 143
11X-RAY DIFFRACTION11C144 - 194
12X-RAY DIFFRACTION12C201
13X-RAY DIFFRACTION13D6 - 57
14X-RAY DIFFRACTION14D58 - 143
15X-RAY DIFFRACTION15D144 - 193
16X-RAY DIFFRACTION16D201
17X-RAY DIFFRACTION17E4 - 57
18X-RAY DIFFRACTION18E58 - 143
19X-RAY DIFFRACTION19E144 - 193
20X-RAY DIFFRACTION20E201
21X-RAY DIFFRACTION21F7 - 57
22X-RAY DIFFRACTION22F58 - 143
23X-RAY DIFFRACTION23F144 - 192
24X-RAY DIFFRACTION24F201

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