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- PDB-6jyi: Crystal structure of the PadR-like transcriptional regulator BC17... -

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Basic information

Entry
Database: PDB / ID: 6jyi
TitleCrystal structure of the PadR-like transcriptional regulator BC1756 from Bacillus cereus
ComponentsTranscriptional repressor PadR
KeywordsTRANSCRIPTION / Transcription factor
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 / Transcriptional repressor PadR
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsKim, T.H. / Park, S.C. / Lee, K.C. / Song, W.S. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural and DNA-binding studies of the PadR-like transcriptional regulator BC1756 from Bacillus cereus.
Authors: Kim, T.H. / Park, S.C. / Lee, K.C. / Song, W.S. / Yoon, S.I.
History
DepositionApr 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor PadR
B: Transcriptional repressor PadR


Theoretical massNumber of molelcules
Total (without water)44,3942
Polymers44,3942
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-45 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.682, 132.672, 49.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 33
2116B1 - 33
1216A36 - 59
2216B36 - 59
1316A68 - 89
2316B68 - 89
1126A90 - 127
2126B90 - 127
1226A145 - 200
2226B145 - 200

NCS ensembles :
ID
1
2

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Components

#1: Protein Transcriptional repressor PadR


Mass: 22197.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_1756 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81F45
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 3350, sodium citrate, ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97939 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 31084 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 43.9
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3033 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.845 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24672 1562 5 %RANDOM
Rwork0.20684 ---
obs0.20884 29372 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 0 141 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222852
X-RAY DIFFRACTIONr_bond_other_d0.0010.022018
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9743825
X-RAY DIFFRACTIONr_angle_other_deg0.86434904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8295339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56624.203138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03815557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0411517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
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_it0.8231.51682
X-RAY DIFFRACTIONr_mcbond_other0.2211.5693
X-RAY DIFFRACTIONr_mcangle_it1.50622710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.51231170
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9744.51113
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
11A1049loose positional0.765
22A844loose positional0.385
11B1049loose thermal2.4410
22B844loose thermal2.7310
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 103 -
Rwork0.303 2092 -
obs--96.78 %
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)
13.0979-1.5162-1.52270.86260.59761.5129-0.2067-0.47820.40890.31090.2095-0.34040.01660.2583-0.00290.29360.009-0.11290.2347-0.06750.29548.38134.7319.594
22.87840.2986-0.84071.31160.23816.29080.11830.02960.08290.35060.05140.0158-0.015-0.2036-0.16970.2512-0.02590.01210.06-0.0030.059124.8250.35618.961
31.9357-0.966-0.86132.07650.61681.24510.03620.1110.47940.0543-0.01-0.0638-0.1873-0.0296-0.02620.1182-0.0012-0.06180.09610.04390.224847.00949.8360.557
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 170
2X-RAY DIFFRACTION2B2 - 89
3X-RAY DIFFRACTION3B90 - 173

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