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- PDB-1tlv: Structure of the native and inactive LicT PRD from B. subtilis -

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Basic information

Entry
Database: PDB / ID: 1tlv
TitleStructure of the native and inactive LicT PRD from B. subtilis
ComponentsTranscription antiterminator licT
KeywordsTRANSCRIPTION / transcriptional antitermination / conformational change / LicT / histidine phosphorylation / activation mechanism / HPr / dimer structure / phosphoenolpyruvate (PEP): sugar phosphotransferase system (PTS) / PTS regulation domains (PRD)
Function / homology
Function and homology information


positive regulation of DNA-templated transcription / RNA binding
Similarity search - Function
PRD domain / PTS-regulatory domain, PRD / Transcription antiterminator, conserved site / CAT RNA-binding domain / CAT RNA-binding domain superfamily / CAT RNA binding domain / PRD domain signature. / CAT RNA binding domain / PRD domain / PRD domain ...PRD domain / PTS-regulatory domain, PRD / Transcription antiterminator, conserved site / CAT RNA-binding domain / CAT RNA-binding domain superfamily / CAT RNA binding domain / PRD domain signature. / CAT RNA binding domain / PRD domain / PRD domain / PRD domain superfamily / PRD domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription antiterminator LicT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsGraille, M. / Zhou, C.-Z. / Receveur-Brechot, V. / Collinet, B. / Declerck, N. / van Tilbeurgh, H.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Activation of the LicT Transcriptional Antiterminator Involves a Domain Swing/Lock Mechanism Provoking Massive Structural Changes
Authors: Graille, M. / Zhou, C.-Z. / Receveur-Brechot, V. / Collinet, B. / Declerck, N. / van Tilbeurgh, H.
#1: Journal: Embo J. / Year: 2001
Title: Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator
Authors: van Tilbeurgh, H. / Lecoq, D. / Declerck, N.
History
DepositionJun 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription antiterminator licT


Theoretical massNumber of molelcules
Total (without water)26,1891
Polymers26,1891
Non-polymers00
Water1,76598
1
A: Transcription antiterminator licT

A: Transcription antiterminator licT


Theoretical massNumber of molelcules
Total (without water)52,3782
Polymers52,3782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3490 Å2
ΔGint-24 kcal/mol
Surface area19710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.734, 48.734, 162.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, z.

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Components

#1: Protein Transcription antiterminator licT


Mass: 26189.223 Da / Num. of mol.: 1 / Fragment: PTS-REGULATORY DOMAIN (RESIDUES 57-274)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: LICT, N15A, BSU39080 / Production host: Escherichia coli (E. coli) / References: UniProt: P39805
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.8 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: 0.5-0.7 M potassium acetate, 0.1 M sodium citrate, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.9→99 Å / Num. obs: 18537 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.59 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.036 / Net I/σ(I): 44.7
Reflection shellResolution: 1.9→1.96 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.401 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→9.9 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 558117.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 821 5 %RANDOM
Rwork0.269 ---
obs0.269 16547 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.8314 Å2 / ksol: 0.420091 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å2-1.78 Å20 Å2
2---2.1 Å20 Å2
3---4.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.95→9.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 0 98 1806
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 132 5.1 %
Rwork0.326 2441 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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