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- PDB-5dym: Crystal structure of a PadR family transcription regulator from h... -

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Basic information

Entry
Database: PDB / ID: 5dym
TitleCrystal structure of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291 - CdPadR_0991 to 1.89 Angstrom resolution
ComponentsPadR-family transcriptional regulator
KeywordsDNA BINDING PROTEIN / PadR / wHTH DNA binding domain / Helix turn helix motifs / transcription regulator / PadR-s2
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / PadR-family transcriptional regulator
Function and homology information
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.894 Å
AuthorsIsom, C.E. / Karr, E.A. / Menon, S.K. / West, A.H. / Richter-Addo, G.B.
CitationJournal: Bmc Microbiol. / Year: 2016
Title: Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291.
Authors: Isom, C.E. / Menon, S.K. / Thomas, L.M. / West, A.H. / Richter-Addo, G.B. / Karr, E.A.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PadR-family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)14,1121
Polymers14,1121
Non-polymers00
Water64936
1
A: PadR-family transcriptional regulator

A: PadR-family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)28,2252
Polymers28,2252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2420 Å2
ΔGint-21 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.420, 92.420, 40.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-236-

HOH

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Components

#1: Protein PadR-family transcriptional regulator


Mass: 14112.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain R20291) (bacteria)
Strain: R20291 / Gene: CDR20291_0991 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: C9YK90
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 65.1 % / Description: Square/bipyramidal, clear
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.1 M NaCl, 100 mM HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.2 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.894→34.37 Å / Num. obs: 14302 / % possible obs: 99 % / Redundancy: 2 % / Rmerge(I) obs: 0.018 / Net I/σ(I): 20.27
Reflection shellResolution: 1.894→1.962 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3821 / Mean I/σ(I) obs: 2.15 / % possible all: 95.07

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XMA

1xma


Resolution: 1.894→34.369 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 749 5.24 %
Rwork0.213 --
obs0.2146 14293 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.894→34.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 0 36 844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008835
X-RAY DIFFRACTIONf_angle_d0.9311111
X-RAY DIFFRACTIONf_dihedral_angle_d14.741335
X-RAY DIFFRACTIONf_chiral_restr0.044113
X-RAY DIFFRACTIONf_plane_restr0.004139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8944-2.04070.28791450.24552605X-RAY DIFFRACTION97
2.0407-2.2460.25681360.21732687X-RAY DIFFRACTION99
2.246-2.57090.2571590.22342680X-RAY DIFFRACTION100
2.5709-3.23870.27291610.23332706X-RAY DIFFRACTION100
3.2387-34.37430.22011480.19742866X-RAY DIFFRACTION99

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