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- PDB-4l51: Crystal structures of the LsrR proteins complexed with phospho-AI... -

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Basic information

Entry
Database: PDB / ID: 4l51
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 / DNA 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
5-O-phosphono-alpha-D-ribofuranose / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Transcriptional regulator LsrR
B: Transcriptional regulator LsrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3084
Polymers55,8482
Non-polymers4602
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-17 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.613, 116.613, 79.744
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: Sugar ChemComp-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 56.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Bis-Tris, 9.1% PEG3350, 0.01M Barium chloride dehydrate, 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-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→42.7 Å / Num. all: 48351 / Num. obs: 45849 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→1.97 Å / % possible all: 98.4

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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→42.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.721 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20387 2431 5 %RANDOM
Rwork0.16605 ---
obs0.16795 45849 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å20 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 28 328 3976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023717
X-RAY DIFFRACTIONr_bond_other_d0.0020.023725
X-RAY DIFFRACTIONr_angle_refined_deg2.061.9845031
X-RAY DIFFRACTIONr_angle_other_deg0.9833.0038523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.41224.514144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05815642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3831526
X-RAY DIFFRACTIONr_chiral_restr0.1390.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024288
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02810
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 185 -
Rwork0.233 3342 -
obs--98.19 %

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