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- PDB-4l4z: Crystal structures of the LsrR proteins complexed with phospho-AI... -

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Basic information

Entry
Database: PDB / ID: 4l4z
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
Chem-D5X / Transcriptional regulator LsrR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-16 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.689, 117.689, 79.372
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: Chemical ChemComp-D5X / (2S)-2,3,3-trihydroxy-4-oxopentyl dihydrogen phosphate


Mass: 230.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
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: 1.1 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: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→34.68 Å / Num. all: 26903 / Num. obs: 25502 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.38 Å / % possible all: 91.3

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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: 2.3→34.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.882 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23251 1357 5.1 %RANDOM
Rwork0.1719 ---
obs0.17492 25502 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.354 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.35 Å20 Å2
2---0.35 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 28 173 3852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193743
X-RAY DIFFRACTIONr_bond_other_d0.0010.023747
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.9815070
X-RAY DIFFRACTIONr_angle_other_deg0.8963.0018573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1915505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.81124.726146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83915647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6971525
X-RAY DIFFRACTIONr_chiral_restr0.1580.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
LS refinement shellResolution: 2.302→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 96 -
Rwork0.208 1778 -
obs--90.53 %

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