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- PDB-3zkc: Crystal structure of the master regulator for biofilm formation S... -

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Basic information

Entry
Database: PDB / ID: 3zkc
TitleCrystal structure of the master regulator for biofilm formation SinR in complex with DNA.
Components
  • 5'-D(*AP*AP*AP*GP*TP*TP*CP*TP*CP*TP*TP*TP*AP*GP *AP*GP*AP*AP*CP*AP*AP)-3'
  • 5'-D(*AP*TP*TP*GP*TP*TP*CP*TP*CP*TP*AP*AP*AP*GP *AP*GP*AP*AP*CP*TP*TP)-3'
  • HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / BIOFILM / HTH TYPE TRANSCRIPTIONAL REPRESSOR
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
SinR repressor/SinI anti-repressor, dimerisation domain / SinR repressor/SinI anti-repressor, dimerisation domain superfamily / Anti-repressor SinI / Sin domain profile. / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...SinR repressor/SinI anti-repressor, dimerisation domain / SinR repressor/SinI anti-repressor, dimerisation domain superfamily / Anti-repressor SinI / Sin domain profile. / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH-type transcriptional regulator SinR
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNewman, J.A. / Rodrigues, C. / Lewis, R.J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Molecular Basis of the Activity of Sinr, the Master Regulator of Biofilm Formation in Bacillus Subtilis.
Authors: Newman, J.A. / Rodrigues, C. / Lewis, R.J.
History
DepositionJan 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR
C: 5'-D(*AP*AP*AP*GP*TP*TP*CP*TP*CP*TP*TP*TP*AP*GP *AP*GP*AP*AP*CP*AP*AP)-3'
D: 5'-D(*AP*TP*TP*GP*TP*TP*CP*TP*CP*TP*AP*AP*AP*GP *AP*GP*AP*AP*CP*TP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)38,9104
Polymers38,9104
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-51.3 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.364, 79.739, 67.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR


Mass: 13009.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P06533
#2: DNA chain 5'-D(*AP*AP*AP*GP*TP*TP*CP*TP*CP*TP*TP*TP*AP*GP *AP*GP*AP*AP*CP*AP*AP)-3'


Mass: 6454.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) BACILLUS SUBTILIS (bacteria)
#3: DNA chain 5'-D(*AP*TP*TP*GP*TP*TP*CP*TP*CP*TP*AP*AP*AP*GP *AP*GP*AP*AP*CP*TP*TP)-3'


Mass: 6436.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) BACILLUS SUBTILIS (bacteria)

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5
Details: 0.01M ZNCL2, 0.1M SODIUM ACTEATE, PH 5.0, 20% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.977
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2012 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3→40.5 Å / Num. obs: 13020 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 102.38 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B0N

1b0n


Resolution: 3→40.556 Å / SU ML: 0.39 / σ(F): 1.4 / Phase error: 31.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 608 4.7 %
Rwork0.2417 --
obs0.2427 13012 94.71 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.5 Å2
Refinement stepCycle: LAST / Resolution: 3→40.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 856 0 0 1834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031948
X-RAY DIFFRACTIONf_angle_d0.7882803
X-RAY DIFFRACTIONf_dihedral_angle_d23.382793
X-RAY DIFFRACTIONf_chiral_restr0.038322
X-RAY DIFFRACTIONf_plane_restr0.001207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.30190.35731460.33263055X-RAY DIFFRACTION94
3.3019-3.77940.35481640.27183081X-RAY DIFFRACTION94
3.7794-4.76050.29751430.24593152X-RAY DIFFRACTION96
4.7605-40.55960.21611550.22193116X-RAY DIFFRACTION95

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