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- PDB-4l5j: Crystal structures of the LsrR proteins complexed with phospho-AI... -

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Basic information

Entry
Database: PDB / ID: 4l5j
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 / SorC/DeoR family / Helix-Turn-Helix domain
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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Sugar-binding domain, putative / Putative sugar-binding domain / Rossmann fold - #1360 / NagB/RpiA transferase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / 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: 2.6 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 11, 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
C: Transcriptional regulator LsrR
D: Transcriptional regulator LsrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,5888
Polymers135,6674
Non-polymers9204
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-63 kcal/mol
Surface area49010 Å2
MethodPISA
2
A: Transcriptional regulator LsrR
B: Transcriptional regulator LsrR
C: Transcriptional regulator LsrR
D: Transcriptional regulator LsrR
hetero molecules

A: Transcriptional regulator LsrR
B: Transcriptional regulator LsrR
C: Transcriptional regulator LsrR
D: Transcriptional regulator LsrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,17616
Polymers271,3358
Non-polymers1,8418
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area22610 Å2
ΔGint-136 kcal/mol
Surface area94660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.330, 80.611, 118.701
Angle α, β, γ (deg.)90.00, 118.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Transcriptional regulator LsrR


Mass: 33916.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: lsrR, ydeW, b1512, JW1505 / Plasmid: pGEX-4T-1 / 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.: 4
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.: 236 / 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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Bis-Tris, 2% isopropanol, 8% gamma-butyrolactone, 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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→47.32 Å / Num. all: 45073 / Num. obs: 45072 / % possible obs: 78.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 21.7 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 92.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.32 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 206683.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 4553 10.1 %RANDOM
Rwork0.217 ---
obs0.217 45072 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.1477 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 65.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-17.79 Å2
2---4.96 Å20 Å2
3---5.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å0.83 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9216 0 56 236 9508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.428 640 10.1 %
Rwork0.419 5673 -
obs--78 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6r5p_all_cns.paramr5p_all_cns.top

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