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- PDB-4esf: Crystal structure of PadR-like transcriptional regulator (BCE3449... -

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Basic information

Entry
Database: PDB / ID: 4esf
TitleCrystal structure of PadR-like transcriptional regulator (BCE3449) from Bacillus cereus strain ATCC 10987
ComponentsPadR-like transcriptional regulator
KeywordsTRANSCRIPTION / PadR family / transcriptional regulator / DNA binding protein / winged-HTH fold
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 domain-containing protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PadR-like transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)13,7621
Polymers13,7621
Non-polymers00
Water18010
1
A: PadR-like transcriptional regulator

A: PadR-like transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)27,5242
Polymers27,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3060 Å2
ΔGint-33 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.945, 43.945, 120.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PadR-like transcriptional regulator


Mass: 13761.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_3449 / Plasmid: pNSC8048 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): subsp. cremoris NZ9000 / References: UniProt: Q734F6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M imidazole, 9% (w/v) PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING 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: 2.2→43.94 Å / Num. obs: 6500 / % possible obs: 99.7 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 27.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.2-2.327.10.5113.3884198.1
2.32-2.468.10.276.38591100
2.46-2.638.10.1869.38151100
2.63-2.8480.12114.17701100
2.84-3.1180.06724.37251100
3.11-3.487.90.04137.66501100
3.48-4.027.70.02954.45911100
4.02-4.927.60.02269.65091100
4.92-6.967.10.02365.64081100
6.96-43.945.90.02467.6257199.3

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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: 2.2→41.268 Å / SU ML: 0.36 / σ(F): 1.38 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 631 9.81 %
Rwork0.2176 --
obs0.2233 6431 99.23 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.418 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7843 Å20 Å2-0 Å2
2--7.7843 Å20 Å2
3----15.5686 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 0 10 835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01838
X-RAY DIFFRACTIONf_angle_d1.011123
X-RAY DIFFRACTIONf_dihedral_angle_d15.088322
X-RAY DIFFRACTIONf_chiral_restr0.057127
X-RAY DIFFRACTIONf_plane_restr0.004137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.37030.39291170.25311093X-RAY DIFFRACTION98
2.3703-2.60880.34181300.24041129X-RAY DIFFRACTION99
2.6088-2.98620.30651270.2371141X-RAY DIFFRACTION100
2.9862-3.76190.27621340.20961163X-RAY DIFFRACTION100
3.7619-41.27530.24521230.20951274X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.8414-1.4427-1.15994.28771.76849.13480.26510.5337-0.4169-0.185-0.14180.518-0.0452-0.8739-0.13330.3919-0.0755-0.05110.37990.09390.3297-1.100619.0679-9.0211
21.59640.58442.06882.4167-1.61992.54830.3312-0.73740.5910.1005-0.0389-0.5913-0.0797-0.1427-0.28180.5214-0.0743-0.00480.2964-0.02050.3310.731919.93214.6297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:77)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 78:107)

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