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- PDB-5x13: Crystal structure of Bacillus subtilis PadR in complex with p-cou... -

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Basic information

Entry
Database: PDB / ID: 5x13
TitleCrystal structure of Bacillus subtilis PadR in complex with p-coumaric acid
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION / Transcription factor
Function / homology
Function and homology information


Transcription regulator PadR, C-terminal / Virulence activator alpha C-term / 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
4'-HYDROXYCINNAMIC ACID / Transcriptional regulator
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii strain W23 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPark, S.C. / Kwak, Y.M. / Song, W.S. / Hong, M. / Yoon, S.I.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR
Authors: Park, S.C. / Kwak, Y.M. / Song, W.S. / Hong, M. / Yoon, S.I.
History
DepositionJan 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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
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: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0073
Polymers21,7511
Non-polymers2562
Water3,153175
1
A: Transcriptional regulator
hetero molecules

A: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0146
Polymers43,5022
Non-polymers5134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8330 Å2
ΔGint-37 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.514, 75.450, 38.125
Angle α, β, γ (deg.)90.00, 96.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional regulator


Mass: 21750.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii strain W23 (bacteria)
Strain: W23 / Gene: padR, BSUW23_04210 / Production host: Escherichia coli (E. coli) / References: UniProt: E0TW95
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 10 mM p-coumaric acid, 22% PEG 3350, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 23666 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 40.2
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.224

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X12

5x12


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.506 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.19533 1214 5.1 %RANDOM
Rwork0.1678 ---
obs0.16925 22412 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.31 Å2
2--0.31 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 18 175 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221546
X-RAY DIFFRACTIONr_bond_other_d0.0010.021087
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9882091
X-RAY DIFFRACTIONr_angle_other_deg0.91832662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1555193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22824.0367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66615294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.786157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021694
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02322
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.931.5915
X-RAY DIFFRACTIONr_mcbond_other0.3081.5366
X-RAY DIFFRACTIONr_mcangle_it1.64921479
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5673631
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0674.5605
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 104 -
Rwork0.254 1622 -
obs--99.54 %
Refinement TLS params.

T23: -0.0007 Å2 / 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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.92470.9739-0.11063.60470.22771.5864-0.11230.0985-0.0546-0.39460.0553-0.20970.10090.00190.0570.2563-0.02950.10950.04780.0722-19.353-25.3459.195
20.9454-0.05350.15220.2329-0.08960.5393-0.01550.0967-0.00420.0033-0.005-0.0196-0.04350.03730.02050.2139-0.00450.08690.03860.04181.274-6.27814.029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 86
2X-RAY DIFFRACTION2A87 - 182

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