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- PDB-6azh: Clostridium perfringens putative fatty acid metabolism regulator -

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Basic information

Entry
Database: PDB / ID: 6azh
TitleClostridium perfringens putative fatty acid metabolism regulator
ComponentsTetR family transcriptional regulator
KeywordsTRANSCRIPTION / Regulator
Function / homologyHomeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsWilliam, W.G. / Redinbo, M.R.
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 11, 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 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: TetR family transcriptional regulator
B: TetR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)44,8682
Polymers44,8682
Non-polymers00
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-28 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.869, 93.873, 55.067
Angle α, β, γ (deg.)90.00, 96.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TetR family transcriptional regulator


Mass: 22434.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: BXT94_00180 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9V3V3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97935 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.68→29.104 Å / Num. obs: 39564 / % possible obs: 97.5 % / Redundancy: 7.1 % / Net I/σ(I): 23.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementResolution: 1.75→29.104 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.35
RfactorNum. reflection% reflection
Rfree0.2253 1999 5.09 %
Rwork0.1964 --
obs0.1979 39276 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→29.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 0 395 3429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073097
X-RAY DIFFRACTIONf_angle_d0.7434157
X-RAY DIFFRACTIONf_dihedral_angle_d2.4192275
X-RAY DIFFRACTIONf_chiral_restr0.047472
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.28531430.23212667X-RAY DIFFRACTION98
1.7938-1.84230.3141440.24382700X-RAY DIFFRACTION98
1.8423-1.89650.33471450.27082689X-RAY DIFFRACTION97
1.8965-1.95770.38161270.35632357X-RAY DIFFRACTION87
1.9577-2.02760.2691440.21532683X-RAY DIFFRACTION99
2.0276-2.10880.24871420.23852647X-RAY DIFFRACTION96
2.1088-2.20470.22511450.19822702X-RAY DIFFRACTION99
2.2047-2.32090.28181360.2222545X-RAY DIFFRACTION92
2.3209-2.46630.22071450.19592708X-RAY DIFFRACTION99
2.4663-2.65660.21591460.18192721X-RAY DIFFRACTION99
2.6566-2.92370.18561450.19412716X-RAY DIFFRACTION99
2.9237-3.34620.20311460.19592710X-RAY DIFFRACTION99
3.3462-4.21380.22661430.16662670X-RAY DIFFRACTION96
4.2138-29.10760.17651480.16552762X-RAY DIFFRACTION99

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