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- PDB-3k2n: The crystal structure of sigma-54-dependent transcriptional regul... -

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Basic information

Entry
Database: PDB / ID: 3k2n
TitleThe crystal structure of sigma-54-dependent transcriptional regulator domain from Chlorobium Tepidum TLS
ComponentsSigma-54-dependent transcriptional regulator
Keywordstranscription regulator / sigma-54-dependent transcriptional regulator domain / Chlorobium tepidum TLS / PSI-2 / Protein Structure Initiative / Structural Genomics / Midwest Center for Structural Genomics (MCSG) / ATP-binding / DNA-binding / Nucleotide-binding / Transcription / Transcription regulation / Two-component regulatory system
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / GAF domain ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / GAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sigma-54-dependent transcriptional regulator
Similarity search - Component
Biological speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsWu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of sigma-54-dependent transcriptional regulator domain from Chlorobium
Authors: Wu, R. / Clancy, S. / Joachimiak, A.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sigma-54-dependent transcriptional regulator
B: Sigma-54-dependent transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)39,8242
Polymers39,8242
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-10 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.121, 81.250, 83.522
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 Sigma-54-dependent transcriptional regulator


Mass: 19912.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Strain: taxon:194439 / Gene: CT0108, GAF / Plasmid: PDM68 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8KG60
#2: 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Na acetate, 20% PEG3k, 0.1M Na-Hepes PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 18, 2007 / Details: mirrors
RadiationMonochromator: Si 111, channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 17064 / Num. obs: 16911 / % possible obs: 99.6 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 4.875
Reflection shellResolution: 2.58→2.66 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 6.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
MLPHAREphasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection
RefinementMethod to determine structure: MAD / Resolution: 2.5→45.615 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU ML: 0.41 / σ(F): 1.33 / Phase error: 29.9 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2803 678 5.02 %
Rwork0.1967 --
obs0.2009 13494 99.83 %
all-11428 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.885 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 45.247 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å20 Å2
2--5.3 Å20 Å2
3----3.55 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 0 37 2821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092832
X-RAY DIFFRACTIONf_angle_d1.1733828
X-RAY DIFFRACTIONf_dihedral_angle_d20.2491042
X-RAY DIFFRACTIONf_chiral_restr0.078440
X-RAY DIFFRACTIONf_plane_restr0.003492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.69320.37091220.28462515X-RAY DIFFRACTION99
2.6932-2.96420.34841490.23952497X-RAY DIFFRACTION100
2.9642-3.3930.28651370.20622537X-RAY DIFFRACTION100
3.393-4.27430.30351310.17052579X-RAY DIFFRACTION100
4.2743-45.62220.22771390.1792688X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.86010.2874-0.52230.91920.24991.17590.05420.31140.0573-0.1546-0.0804-0.05290.0301-0.0440.02320.2840.0234-0.04190.3180.02630.243624.202439.567334.1165
21.24670.1019-0.30891.0060.48541.73760.03620.259-0.1103-0.01360.06370.1169-0.0089-0.1727-0.0490.2454-0.0603-0.05640.30430.00970.239
Refinement TLS groupSelection details: chain B

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