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- PDB-5y8t: Crystal structure of Bacillus subtilis PadR in complex with p-cou... -

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Basic information

Entry
Database: PDB / ID: 5y8t
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionAug 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
C: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5815
Polymers65,2533
Non-polymers3282
Water5,477304
1
A: Transcriptional regulator
hetero molecules

A: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8304
Polymers43,5022
Non-polymers3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_857-x+3,y,-z+21
Buried area7850 Å2
ΔGint-38 kcal/mol
Surface area15850 Å2
MethodPISA
2
B: Transcriptional regulator
C: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6663
Polymers43,5022
Non-polymers1641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-42 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.217, 125.301, 79.657
Angle α, β, γ (deg.)90.00, 113.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-478-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
31A
12C
22B
32A
13B
23A

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGHISHISCC2 - 878 - 93
21ARGARGHISHISBB2 - 878 - 93
31ARGARGHISHISAA2 - 878 - 93
12LEULEUASPASPCC100 - 180106 - 186
22LEULEUGLUGLUBB100 - 181106 - 187
32LEULEUASPASPAA100 - 180106 - 186
13GLNGLNMETMETBB88 - 9994 - 105
23GLNGLNMETMETAA88 - 9994 - 105

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Transcriptional regulator


Mass: 21750.912 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (strain ATCC 23059 / NRRL B-14472 / W23) (bacteria)
Strain: ATCC 23059 / NRRL B-14472 / 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.: 2 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 3350, 0.1 M phosphate-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 56648 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 22.8
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.496

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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: 2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.937 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22215 2656 4.7 %RANDOM
Rwork0.19532 ---
obs0.19657 53676 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 31.861 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20.99 Å2
2---0.86 Å20 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 24 304 4388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224192
X-RAY DIFFRACTIONr_bond_other_d0.0010.022935
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.985635
X-RAY DIFFRACTIONr_angle_other_deg0.86637154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3565496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47923.946185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66615789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3241519
X-RAY DIFFRACTIONr_chiral_restr0.0880.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02879
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_it0.7831.52479
X-RAY DIFFRACTIONr_mcbond_other0.2411.51004
X-RAY DIFFRACTIONr_mcangle_it1.41423971
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1831713
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4274.51660
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A422medium positional0.420.5
11B422medium positional0.250.5
11C422medium positional0.250.5
22A458medium positional0.220.5
22B458medium positional0.180.5
22C458medium positional0.130.5
33A70medium positional0.530.5
11A579loose positional0.95
11B579loose positional0.515
11C579loose positional0.55
22A597loose positional0.385
22B597loose positional0.275
22C597loose positional0.245
33A90loose positional1.115
11A422medium thermal0.672
11B422medium thermal0.692
11C422medium thermal0.592
22A458medium thermal0.632
22B458medium thermal0.652
22C458medium thermal0.622
33A70medium thermal1.042
11A579loose thermal0.7710
11B579loose thermal0.7810
11C579loose thermal0.610
22A597loose thermal0.810
22B597loose thermal0.7810
22C597loose thermal0.7510
33A90loose thermal0.8310
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 205 -
Rwork0.254 3921 -
obs--99.95 %
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)
14.2875-0.7017-3.72888.75023.80610.8324-0.18210.3334-0.4809-0.9483-0.01350.75130.0108-0.65420.19560.3151-0.0699-0.01610.20010.06720.245889.644-23.2679.244
22.30171.729-0.18687.0561-0.39980.86390.0651-0.04960.03190.2633-0.1895-0.3379-0.1370.15540.12440.1617-0.043-0.05910.09630.04730.1108102.55128.88344.894
35.1307-0.6562-1.221.92110.24983.46320.17280.84380.0188-0.3022-0.1213-0.0062-0.06580.0917-0.05140.12940.03250.05830.292-0.020.0684104.596-4.39423.875
42.2763-0.2897-0.34370.45140.25141.95620.10180.19930.0069-0.01250.05040.01270.0341-0.0926-0.15220.09390.00180.03250.09170.01380.0297106.401-5.28567.216
50.9659-0.24560.07721.92250.55061.9214-0.0709-0.0325-0.01140.28620.01270.0123-0.06590.10270.05820.0974-0.00310.01460.03970.00140.01495.9511.44448.288
60.9340.03580.36492.1139-0.16770.7758-0.030.07640.03070.0084-0.06340.2668-0.0534-0.03250.09350.0710.00040.01950.0603-0.01530.062787.4165.95442.035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 86
2X-RAY DIFFRACTION2B2 - 86
3X-RAY DIFFRACTION3C2 - 86
4X-RAY DIFFRACTION4A87 - 180
5X-RAY DIFFRACTION5B87 - 181
6X-RAY DIFFRACTION6C87 - 180

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