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- PDB-5x12: Crystal structure of Bacillus subtilis PadR -

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Basic information

Entry
Database: PDB / ID: 5x12
TitleCrystal structure of Bacillus subtilis PadR
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
Transcriptional regulator
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii strain W23 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)21,7511
Polymers21,7511
Non-polymers00
Water2,990166
1
A: Transcriptional regulator

A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,5022
Polymers43,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6830 Å2
ΔGint-45 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.063, 75.480, 38.017
Angle α, β, γ (deg.)90.00, 96.43, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% 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: Apr 9, 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: 23797 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 38.6
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.278

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.263 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20347 1215 5.1 %RANDOM
Rwork0.17013 ---
obs0.17184 22518 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 166 1610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221510
X-RAY DIFFRACTIONr_bond_other_d0.0010.021058
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.982044
X-RAY DIFFRACTIONr_angle_other_deg0.932593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8565190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3752465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35715288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.81157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021647
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02309
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_it0.9721.5908
X-RAY DIFFRACTIONr_mcbond_other0.3061.5364
X-RAY DIFFRACTIONr_mcangle_it1.71721467
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6263602
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2224.5570
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
Rfree0.267 82 -
Rwork0.254 1647 -
obs--98.74 %
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)
11.61820.40020.0694.83820.40131.6541-0.14020.1072-0.0218-0.47560.1096-0.31480.00320.06670.03050.1625-0.05080.08020.0458-0.00370.087-19.525-25.3339.166
21.6787-0.20390.18460.2738-0.05690.5475-0.00160.1508-0.0416-0.00710.0137-0.0146-0.00290.0246-0.01210.1085-0.00740.0320.0217-0.00250.02051.161-6.28113.939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 86
2X-RAY DIFFRACTION2A87 - 182

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