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- PDB-1h99: PRD of LicT antiterminator from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1h99
TitlePRD of LicT antiterminator from Bacillus subtilis
ComponentsTRANSCRIPTION ANTITERMINATOR LICT
KeywordsTRANSCRIPTIONAL ANTITERMINATOR / PTS REGULATORY DOMAIN
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 / MAD / Resolution: 1.55 Å
AuthorsVan Tilbeurgh, H. / Declerck, N.
CitationJournal: Embo J. / Year: 2001
Title: Crystal Structure of an Activated Form of the Pts Regulation Domain from the Lict Transcriptional Antitrminator
Authors: Van Tilbeurgh, H. / Lecoq, D. / Declerck, N.
History
DepositionMar 6, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)26,3971
Polymers26,3971
Non-polymers00
Water3,441191
1
A: TRANSCRIPTION ANTITERMINATOR LICT

A: TRANSCRIPTION ANTITERMINATOR LICT


Theoretical massNumber of molelcules
Total (without water)52,7952
Polymers52,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)78.250, 129.710, 50.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein TRANSCRIPTION ANTITERMINATOR LICT / LICT-ANTITERMINATOR


Mass: 26397.344 Da / Num. of mol.: 1 / Fragment: PTS-REGULATORY DOMAIN RESIDUES 57-277 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Gene: LICT / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P39805
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION HIS207ASP, HIS269ASP POSITIVE REGULATION OF THE GLUCANASE OPERON (LICST)

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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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growpH: 5 / Details: 200 MM MG(AC)2, 10% PEG8000, pH 5.00
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1300 mM1dropNaCl
25 mMdithiothreitol1drop
310 mMTris1drop
46 mg/mlprotein1drop
5200 mM1reservoirMgAc2
6100 mMcacodylate1reservoir
710 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979, 0.979, 0.886
DetectorDate: Nov 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.8861
ReflectionResolution: 1.55→20 Å / Num. obs: 37674 / % possible obs: 99.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.6
Reflection shellResolution: 1.55→1.65 Å / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 4.4 / % possible all: 98.2
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→19.98 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2640 7 %RANDOM
Rwork0.224 ---
obs0.224 37578 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.2798 Å2 / ksol: 0.345048 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2---1.44 Å20 Å2
3----0.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.55→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 0 191 2018
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_d18.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it3.642
X-RAY DIFFRACTIONc_scangle_it4.062.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.232 446 7.3 %
Rwork0.218 5647 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69

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