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- PDB-4g12: Crystal structure of putative TetR family transcriptional regulat... -

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Basic information

Entry
Database: PDB / ID: 4g12
TitleCrystal structure of putative TetR family transcriptional regulator, Fad35R, from Mycobacterium tuberculosis
ComponentsProbable transcriptional regulatory protein (Probably TETR-FAMILY)
KeywordsDNA BINDING PROTEIN / OHM fold / Fatty Acid Binding domain
Function / homology
Function and homology information


evasion of host immune response / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function
HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, 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. / Homeodomain-like / Homeobox-like domain superfamily ...HTH-type transcriptional repressor KstR2, C-terminal / Tetracyclin repressor-like, 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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TetR-family transcriptional regulator / Probable transcriptional regulatory protein (Probably TetR-family)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.44 Å
AuthorsSingh, A.K. / Manjasetty, B.A. / Singh, V. / Mittal, M. / Kumaran, S.
CitationJournal: to be published
Title: Crystal structure of putative TetR family transcriptional regulator, Fad35R, from Mycobacterium tuberculosis
Authors: Singh, A.K. / Manjasetty, B.A. / Singh, V. / Mittal, M. / Kumaran, S.
History
DepositionJul 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable transcriptional regulatory protein (Probably TETR-FAMILY)
B: Probable transcriptional regulatory protein (Probably TETR-FAMILY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0674
Polymers46,8832
Non-polymers1842
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-23 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.836, 83.211, 95.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable transcriptional regulatory protein (Probably TETR-FAMILY) / Fad35R


Mass: 23441.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Ra / Gene: Rv2506 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06169, UniProt: A5U5K3*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M tri-Sodium citrate, 0.1M Tris-HCl pH 8.5, 30%(v/v) PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97755 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 24, 2012 / Details: mirrors
RadiationMonochromator: Chanel cut Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97755 Å / Relative weight: 1
ReflectionResolution: 3.44→50 Å / Num. obs: 15712 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 64.5 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 12.4
Reflection shellResolution: 3.44→3.5 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.54 / Num. unique all: 782 / Rsym value: 0.529 / % possible all: 98

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXSuite (CCP4)model building
REFMAC5.6.0116refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSuite (CCP4)phasing
RefinementMethod to determine structure: SAD / Resolution: 3.44→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 54.458 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25596 944 11.1 %RANDOM
Rwork0.20759 ---
all0.21301 ---
obs0.21301 7538 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.157 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 3.44→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 12 0 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192901
X-RAY DIFFRACTIONr_bond_other_d0.0010.021968
X-RAY DIFFRACTIONr_angle_refined_deg0.8621.9793928
X-RAY DIFFRACTIONr_angle_other_deg0.81734739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1015382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.76621.545123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68515443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9561538
X-RAY DIFFRACTIONr_chiral_restr0.0440.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
X-RAY DIFFRACTIONr_rigid_bond_restr2.73334869
X-RAY DIFFRACTIONr_sphericity_bonded9.6754831
LS refinement shellResolution: 3.44→3.526 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 69 -
Rwork0.279 465 -
obs-782 99.44 %
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)
11.12170.5001-0.46622.25680.99042.1293-0.35570.01660.0208-0.28490.45010.0337-0.02980.2969-0.09440.1341-0.01350.01930.18630.04010.137141.46438.761532.2302
21.03530.84830.25432.4325-0.89691.728-0.33550.01090.0251-0.09670.299-0.0178-0.3323-0.20760.03650.1490.0435-0.00760.1038-0.02650.123834.830431.096432.1686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 215
2X-RAY DIFFRACTION2B24 - 215

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