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- PDB-4l4y: Crystal structures of the LsrR proteins complexed with phospho-AI... -

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Basic information

Entry
Database: PDB / ID: 4l4y
TitleCrystal structures of the LsrR proteins complexed with phospho-AI-2 and its two different analogs reveal distinct mechanisms for ligand recognition
ComponentsTranscriptional regulator LsrR
KeywordsTRANSCRIPTION REGULATOR / Transcriptional regulator / Phospho-AI-2 binding / DNA binding / removed Helix-turn-Helix domain / SorC/DeoR family
Function / homology
Function and homology information


regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / response to heat / carbohydrate binding / DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Sugar-binding domain, putative / Putative sugar-binding domain / Rossmann fold - #1360 / NagB/RpiA transferase-like / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator LsrR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRyu, K.S. / Ha, J.H. / Eo, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Crystal Structures of the LsrR Proteins Complexed with Phospho-AI-2 and Two Signal-Interrupting Analogues Reveal Distinct Mechanisms for Ligand Recognition.
Authors: Ha, J.H. / Eo, Y. / Grishaev, A. / Guo, M. / Smith, J.A. / Sintim, H.O. / Kim, E.H. / Cheong, H.K. / Bentley, W.E. / Ryu, K.S.
History
DepositionJun 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator LsrR
B: Transcriptional regulator LsrR


Theoretical massNumber of molelcules
Total (without water)55,8482
Polymers55,8482
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-17 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.812, 115.812, 80.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Transcriptional regulator LsrR


Mass: 27924.129 Da / Num. of mol.: 2 / Fragment: UNP residues 53-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: lsrR, ydeW, b1512, JW1505 / Production host: Escherichia coli (E. coli) / References: UniProt: P76141
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 56.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 5% PEG3350, 0.1 M Bis-Tris, 0.1 M NaCl, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.9→27.27 Å / Num. all: 46931 / Num. obs: 44511 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→1.95 Å / % possible all: 90.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.408 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22185 2369 5.1 %RANDOM
Rwork0.17705 ---
obs0.1793 44511 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.34 Å20 Å2
2--0.34 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 0 268 3748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193538
X-RAY DIFFRACTIONr_bond_other_d0.0020.023573
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9774781
X-RAY DIFFRACTIONr_angle_other_deg0.938166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7125478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16524.444135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44315613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1781524
X-RAY DIFFRACTIONr_chiral_restr0.1140.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02772
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 167 -
Rwork0.312 3068 -
obs--89.79 %

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