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- PDB-6ayi: Escherichia coli GusR -

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Basic information

Entry
Database: PDB / ID: 6ayi
TitleEscherichia coli GusR
ComponentsHTH-type transcriptional regulator UidR
KeywordsTRANSCRIPTION / Transcriptional Repressor Protein / Glucuronide Binding Protein / DNA Binding Protein
Function / homology
Function and homology information


DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
4-nitrophenyl beta-D-glucopyranosiduronic acid / HTH-type transcriptional regulator UidR
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLittle, M.S. / Pellock, S.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for the regulation of beta-glucuronidase expression by human gut Enterobacteriaceae.
Authors: Little, M.S. / Pellock, S.J. / Walton, W.G. / Tripathy, A. / Redinbo, M.R.
History
DepositionSep 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 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: HTH-type transcriptional regulator UidR
B: HTH-type transcriptional regulator UidR
C: HTH-type transcriptional regulator UidR
D: HTH-type transcriptional regulator UidR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6478
Polymers88,3864
Non-polymers1,2614
Water5,386299
1
A: HTH-type transcriptional regulator UidR
B: HTH-type transcriptional regulator UidR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8234
Polymers44,1932
Non-polymers6302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-32 kcal/mol
Surface area13690 Å2
MethodPISA
2
C: HTH-type transcriptional regulator UidR
D: HTH-type transcriptional regulator UidR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8234
Polymers44,1932
Non-polymers6302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-32 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.997, 106.744, 135.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein
HTH-type transcriptional regulator UidR / Uid operon repressor


Mass: 22096.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: uidR, Z2623, ECs2326 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P0ACT8
#2: Sugar
ChemComp-C3G / 4-nitrophenyl beta-D-glucopyranosiduronic acid / 4-nitrophenyl beta-D-glucosiduronic acid / 4-nitrophenyl D-glucosiduronic acid / 4-nitrophenyl glucosiduronic acid


Type: D-saccharide / Mass: 315.233 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H13NO9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 8000, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.09→29.181 Å / Num. obs: 43883 / % possible obs: 94.69 % / Redundancy: 2 % / Biso Wilson estimate: 33.15 Å2 / Net I/σ(I): 14.03

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→29.18 Å / SU ML: 0.186 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.3
RfactorNum. reflection% reflection
Rfree0.2212 1911 4.55 %
Rwork0.1868 --
obs0.1883 42020 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.29 Å2
Refinement stepCycle: LAST / Resolution: 2.09→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 88 299 5429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001804236604975200
X-RAY DIFFRACTIONf_angle_d0.3743241913547008
X-RAY DIFFRACTIONf_chiral_restr0.0332734376354818
X-RAY DIFFRACTIONf_plane_restr0.00253093172602906
X-RAY DIFFRACTIONf_dihedral_angle_d3.916057831433188
LS refinement shellResolution: 2.093→2.1453 Å
RfactorNum. reflection% reflection
Rfree0.3111 108 -
Rwork0.273 2262 -
obs--75.99 %
Refinement TLS params.Method: refined / Origin x: 61.034141451 Å / Origin y: 34.5227806903 Å / Origin z: 140.646276914 Å
111213212223313233
T0.254170144655 Å20.00190396569137 Å2-0.0290998318837 Å2-0.225284086944 Å20.0172155218832 Å2--0.245786770548 Å2
L0.514404450168 °20.046692065668 °2-0.0221536704653 °2-0.18869248872 °2-0.0258675601315 °2--0.160317480086 °2
S0.0152650359721 Å °0.00367586589653 Å °-0.0744907463514 Å °0.0291339692217 Å °-0.0175359487463 Å °0.0044910597185 Å °0.0628807452017 Å °0.0357186530571 Å °-7.01639593996E-6 Å °
Refinement TLS groupSelection details: all

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