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- PDB-4lfu: Crystal structure of Escherichia coli SdiA in the space group C2 -

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Basic information

Entry
Database: PDB / ID: 4lfu
TitleCrystal structure of Escherichia coli SdiA in the space group C2
ComponentsRegulatory protein SdiA
KeywordsDNA BINDING PROTEIN / LuxR-type quorum sensing receptor / transcription factor
Function / homology
Function and homology information


positive regulation of DNA-templated transcription initiation / cell cycle / cell division / DNA binding
Similarity search - Function
Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector ...Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Regulatory protein SdiA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsKim, T. / Duong, T. / Wu, C.A. / Choi, J. / Lan, N. / Kang, S.W. / Lokanath, N.K. / Shin, D. / Hwang, H.Y. / Kim, K.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural insights into the molecular mechanism of Escherichia coli SdiA, a quorum-sensing receptor
Authors: Kim, T. / Duong, T. / Wu, C.A. / Choi, J. / Lan, N. / Kang, S.W. / Lokanath, N.K. / Shin, D. / Hwang, H.Y. / Kim, K.K.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

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Assembly

Deposited unit
A: Regulatory protein SdiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6805
Polymers29,2201
Non-polymers4594
Water1,892105
1
A: Regulatory protein SdiA
hetero molecules

A: Regulatory protein SdiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,36010
Polymers58,4412
Non-polymers9198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4140 Å2
ΔGint-44 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.284, 68.691, 69.278
Angle α, β, γ (deg.)90.00, 126.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Regulatory protein SdiA


Mass: 29220.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1916, JW1901, sdiA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07026
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid, 0.2M Lithium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→30 Å / Num. all: 16343 / Num. obs: 15672 / % possible obs: 95.9 % / Redundancy: 3.1 % / Rsym value: 0.073 / Net I/σ(I): 14.7
Reflection shellHighest resolution: 2.26 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 1310 / Rsym value: 0.34 / % possible all: 78.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→29.24 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.583 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27564 819 5 %RANDOM
Rwork0.21263 ---
obs0.21573 15522 95.35 %-
all-16343 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.659 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å2-0.57 Å2
2--1.93 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.26→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 28 105 2074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222013
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9592715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1975235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10723.663101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75215352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5251516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021524
X-RAY DIFFRACTIONr_nbd_refined0.2010.2852
X-RAY DIFFRACTIONr_nbtor_refined0.30.21359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3620.24
X-RAY DIFFRACTIONr_mcbond_it0.8641.51228
X-RAY DIFFRACTIONr_mcangle_it1.41821914
X-RAY DIFFRACTIONr_scbond_it2.1383909
X-RAY DIFFRACTIONr_scangle_it3.3864.5801
LS refinement shellResolution: 2.259→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 39 -
Rwork0.277 814 -
obs--68.46 %

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