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- PDB-3ang: Crystal structure of Thermus thermophilus FadR in complex with E.... -

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Basic information

Entry
Database: PDB / ID: 3ang
TitleCrystal structure of Thermus thermophilus FadR in complex with E. coli-derived dodecyl-CoA
ComponentsTranscriptional repressor, TetR family
KeywordsTRANSCRIPTION / All alpha protein / Tetracyclin repressor-like / C-terminal domain / Transcriptional Repressor / DNA Binding / Acyl-CoA
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / TetR/AcrR family transcriptional repressors, C-terminal domain / 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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DODECYL-COA / Transcriptional repressor, TetR family
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsAgari, Y. / Sakamoto, K. / Agari, K. / Kuramitsu, S. / Shinkai, A.
CitationJournal: Microbiology / Year: 2011
Title: TetR-family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation.
Authors: Agari, Y. / Agari, K. / Sakamoto, K. / Kuramitsu, S. / Shinkai, A.
History
DepositionSep 1, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Transcriptional repressor, TetR family
A: Transcriptional repressor, TetR family
D: Transcriptional repressor, TetR family
B: Transcriptional repressor, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6478
Polymers94,8474
Non-polymers3,7994
Water6,035335
1
C: Transcriptional repressor, TetR family
D: Transcriptional repressor, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3234
Polymers47,4242
Non-polymers1,9002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-20 kcal/mol
Surface area20010 Å2
MethodPISA
2
A: Transcriptional repressor, TetR family
B: Transcriptional repressor, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3234
Polymers47,4242
Non-polymers1,9002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-20 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.182, 104.857, 109.816
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
Transcriptional repressor, TetR family


Mass: 23711.828 Da / Num. of mol.: 4 / Fragment: UNP Residues 2-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0101 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli)
Strain (production host): B834 (DE3) transformed by pRARE2 which derived from Rosetta 2 (DE3)
References: UniProt: Q5SM42
#2: Chemical
ChemComp-DCC / DODECYL-COA


Mass: 949.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H58N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Mosaicity (°)
13.0159.140.614
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop8.520% PEG 3350, 0.2M DIAMMONIUM HYDROGEN PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 8.5
2932evaporation8.810% PEG 6000, 0.1M TRIS-HCL, 0.2M DIAMMONIUM HYDROGEN PHOSPHATE, PH 8.8, EVAPORATION, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2007
Details: vertically bent two dimensional focusing mirror coated in Rhodium
RadiationMonochromator: Fixed exit Si double crystal monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionRedundancy: 6.6 % / Av σ(I) over netI: 42.78 / Number: 347357 / Rmerge(I) obs: 0.09 / Χ2: 1.41 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 53003 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.855099.810.0482.4075.9
3.854.8510010.0632.6376.6
3.363.8510010.071.8736.9
3.053.3610010.0851.2277
2.833.0510010.121.0897.1
2.672.8310010.1691.0277.1
2.532.6799.910.2080.9697
2.422.5399.310.2370.936.5
2.332.4294.610.2630.8665.9
2.252.3386.910.2710.8825.2
ReflectionResolution: 2.25→50 Å / Num. all: 55061 / Num. obs: 55061 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.069 / Χ2: 2.154 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.25-2.336.10.2131153071.83997.4
2.33-2.427.20.15814.354491.216100
2.42-2.537.20.12818.154561.285100
2.53-2.677.10.11321.554581.411100
2.67-2.837.10.0962754991.632100
2.83-3.0570.07736.354691.857100
3.05-3.366.90.06946.255162.434100
3.36-3.856.50.0685455293.61599.9
3.85-4.856.30.05662.155823.77999.7
4.85-505.70.04161.957962.89699.3

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.65 / FOM acentric: 0.65 / FOM centric: 0.68 / Reflection: 48664 / Reflection acentric: 44564 / Reflection centric: 4100
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.4-32.7950.880.910.7924001864536
4-6.40.890.90.872206312908
3.2-40.860.870.7889168090826
2.8-3.20.720.720.6987428096646
2.4-2.80.50.50.481445113589862
2.3-2.40.310.310.3669356613322

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.12phasing
RESOLVE2.12phasing
CNS1.3refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→47.31 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7969 / Data cutoff high absF: 2509401 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 5545 10.2 %RANDOM
Rwork0.22 ---
all0.224 54515 --
obs-54515 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.3808 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 125.37 Å2 / Biso mean: 33.2045 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1-7.39 Å20 Å20 Å2
2---12.64 Å20 Å2
3---5.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.25→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 244 335 7007
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it2.882
X-RAY DIFFRACTIONc_scbond_it3.512
X-RAY DIFFRACTIONc_scangle_it4.862.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 879 10.2 %
Rwork0.308 7759 -
all-8638 -
obs-8638 95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6dcc_prodrug.paramdcc_prodrug.top

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