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- PDB-4esb: Crystal structure of PadR-like transcriptional regulator (BC4206)... -

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Basic information

Entry
Database: PDB / ID: 4esb
TitleCrystal structure of PadR-like transcriptional regulator (BC4206) from Bacillus cereus strain ATCC 14579
ComponentsTranscriptional regulator, PadR family
KeywordsTRANSCRIPTION / PadR family / transcriptional regulator / DNA binding protein / winged-HTH fold
Function / homology
Function and homology information


: / Transcription 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
Similarity search - Domain/homology
Transcriptional regulator, PadR family
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFibriansah, G. / Kovacs, A.T. / Kuipers, O.P. / Thunnissen, A.M.W.H.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structures of Two Transcriptional Regulators from Bacillus cereus Define the Conserved Structural Features of a PadR Subfamily.
Authors: Fibriansah, G. / Kovacs, A.T. / Pool, T.J. / Boonstra, M. / Kuipers, O.P. / Thunnissen, A.M.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Derived calculations
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Transcriptional regulator, PadR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7696
Polymers13,3041
Non-polymers4645
Water30617
1
A: Transcriptional regulator, PadR family
hetero molecules

A: Transcriptional regulator, PadR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,53712
Polymers26,6092
Non-polymers92910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4500 Å2
ΔGint-56 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.536, 73.536, 84.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Transcriptional regulator, PadR family


Mass: 13304.294 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_4206 / Plasmid: pNSC8048 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): subsp. cremoris NZ9000 / References: UniProt: Q818P3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.27 Å3/Da / Density % sol: 71.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 27, 2009 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111)and Ge (220) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→44.22 Å / Num. obs: 8474 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.5-2.6480.6112.912031100
2.64-2.880.4054.511381100
2.8-2.997.90.2317.610691100
2.99-3.237.90.16310.710031100
3.23-3.547.80.09618.29301100
3.54-3.957.80.05829.28441100
3.95-4.567.60.03544.37651100
4.56-5.597.50.03445.46591100
5.59-7.917.10.03640.75211100
7.91-44.226.20.02362324199.1

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Processing

Software
NameVersionClassification
DNAdata collection
BALBESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3hhh

3hhh


Resolution: 2.5→36.498 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 392 4.66 %
Rwork0.2011 --
obs0.2023 8418 99.77 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.126 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.3755 Å20 Å2-0 Å2
2--11.3755 Å20 Å2
3----22.751 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 29 17 870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003863
X-RAY DIFFRACTIONf_angle_d0.7021152
X-RAY DIFFRACTIONf_dihedral_angle_d15.622328
X-RAY DIFFRACTIONf_chiral_restr0.039125
X-RAY DIFFRACTIONf_plane_restr0.003140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.86190.27271440.25252585X-RAY DIFFRACTION100
2.8619-3.60520.24711210.19712649X-RAY DIFFRACTION100
3.6052-36.50160.20361270.19142792X-RAY DIFFRACTION100

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