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- PDB-4go1: Crystal Structure of full length transcription repressor LsrR fro... -

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Basic information

Entry
Database: PDB / ID: 4go1
TitleCrystal Structure of full length transcription repressor LsrR from E. coli.
ComponentsTranscriptional regulator LsrR
KeywordsTRANSCRIPTION / HTH motif / SorC/DeoR family / Transcription repressor / p-AI-2
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
Transcriptional regulator LsrR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWu, M. / Tao, Y. / Liu, X. / Zang, J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for Phosphorylated Autoinducer-2 Modulation of the Oligomerization State of the Global Transcription Regulator LsrR from Escherichia coli
Authors: Wu, M. / Tao, Y. / Liu, X. / Zang, J.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,9864
Polymers69,8022
Non-polymers1842
Water19811
1
A: Transcriptional regulator LsrR
B: Transcriptional regulator LsrR
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)139,9728
Polymers139,6044
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area11260 Å2
ΔGint-68 kcal/mol
Surface area49790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.702, 113.866, 185.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Transcriptional regulator LsrR


Mass: 34900.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1512, JW1505, lsrR, ydeW / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P76141
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Hepes, 6%(w/v) PEG8000, 8%(v/v) ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9999 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 17308 / Num. obs: 17219 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.092 / Rsym value: 0.074 / Net I/σ(I): 21.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5.2 / Num. unique all: 831 / % possible all: 95.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W48

2w48


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26759 1236 7.2 %RANDOM
Rwork0.21601 ---
all0.2198 16057 --
obs0.21969 15982 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.592 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2--5.01 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 0 12 11 4452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224489
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.976051
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.4324.162185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.25315792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7681534
X-RAY DIFFRACTIONr_chiral_restr0.0880.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023306
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5811.52906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09724618
X-RAY DIFFRACTIONr_scbond_it1.18631583
X-RAY DIFFRACTIONr_scangle_it2.1514.51433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 80 -
Rwork0.256 1124 -
obs--95.63 %

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