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- PDB-6ayh: Salmonella enterica GusR -

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Basic information

Entry
Database: PDB / ID: 6ayh
TitleSalmonella enterica GusR
ComponentsTetR family transcriptional regulator
KeywordsTRANSCRIPTION / Transcriptional Repressor Protein / Glucuronide Binding Protein / DNA Binding Protein
Function / homology4-nitrophenyl beta-D-glucopyranosiduronic acid / :
Function and homology information
Biological speciesSalmonella choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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 1.3Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9603
Polymers22,5531
Non-polymers4072
Water2,054114
1
A: TetR family transcriptional regulator
hetero molecules

A: TetR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9206
Polymers45,1052
Non-polymers8154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3820 Å2
ΔGint-33 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.686, 55.230, 60.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-500-

HOH

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Components

#1: Protein TetR family transcriptional regulator


Mass: 22552.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Gene: A7R90_09440 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0A1S0ZXA5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-C3G / 4-nitrophenyl beta-D-glucopyranosiduronic acid


Type: D-saccharide / Mass: 315.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO9 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.2M Ammonium Acetate, 0.1M Bis-Tris pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.05→27.62 Å / Num. obs: 20844 / % possible obs: 99.09 % / Redundancy: 5.8 % / Biso Wilson estimate: 21.8340553132 Å2 / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→27.615 Å / SU ML: 0.2101 / Cross valid method: FREE R-VALUE / σ(F): 1.335 / Phase error: 21.123
RfactorNum. reflection% reflection
Rfree0.222 2076 9.96 %
Rwork0.1833 --
obs0.1871 20844 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.65 Å2
Refinement stepCycle: LAST / Resolution: 2.05→27.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 28 114 1592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002724021790541500
X-RAY DIFFRACTIONf_angle_d0.5091570332782035
X-RAY DIFFRACTIONf_chiral_restr0.0337802547616246
X-RAY DIFFRACTIONf_plane_restr0.00306872902639260
X-RAY DIFFRACTIONf_dihedral_angle_d10.6542364253903
LS refinement shellResolution: 2.0546→2.1023 Å
RfactorNum. reflection% reflection
Rfree0.2855 116 -
Rwork0.2812 1120 -
obs--86.92 %
Refinement TLS params.Method: refined / Origin x: 23.9296949365 Å / Origin y: 16.1072807355 Å / Origin z: 19.882878876 Å
111213212223313233
T0.114834591062 Å20.0128718231201 Å2-0.00567637294381 Å2-0.124999881342 Å2-0.0484407643381 Å2--0.120721364124 Å2
L0.673239656807 °20.212888240016 °20.126377290833 °2-0.307872381046 °2-0.0960701548418 °2--0.104359294773 °2
S0.00448568363594 Å °0.177237811711 Å °-0.125382879548 Å °0.0197092868551 Å °-9.24054059013E-5 Å °0.0135158010497 Å °0.00565907309045 Å °0.0364577565946 Å °0.0375070123291 Å °
Refinement TLS groupSelection details: all

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