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- PDB-2yal: SinR, Master Regulator of biofilm formation in Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2yal
TitleSinR, Master Regulator of biofilm formation in Bacillus subtilis
ComponentsHTH-TYPE TRANSCRIPTIONAL REGULATOR SINR
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATOR / ANTAGONIST / SPORULATION
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. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / HTH-type transcriptional regulator SinR
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsColledge, V.L. / Fogg, M.J. / Levdikov, V.M. / Leech, A. / Dodson, E.J. / Wilkinson, A.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure and Organisation of Sinr, the Master Regulator of Biofilm Formation in Bacillus Subtilis.
Authors: Colledge, V.L. / Fogg, M.J. / Levdikov, V.M. / Leech, A. / Dodson, E.J. / Wilkinson, A.J.
History
DepositionFeb 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Structure summary / Version format compliance
Revision 1.2Nov 20, 2019Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9423
Polymers9,8832
Non-polymers591
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-24.6 kcal/mol
Surface area5170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.117, 36.117, 250.342
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.77051, 0.3865, 0.50689), (0.35904, -0.39393, 0.84612), (0.5267, 0.83393, 0.16476)
Vector: 7.49792, -8.23566, 2.7411)

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Components

#1: Protein/peptide HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR / SINR


Mass: 4941.554 Da / Num. of mol.: 2 / Fragment: OLIGOMERISATION DOMAIN, RESIDUES 75-111
Source method: isolated from a genetically manipulated source
Details: GPA TAG AT N-TERMINUS, NI BOUND BETWEEN N-TERMINI OF A CHAIN AND SYMMETRY EQUIVALENT OF THE B CHAIN
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06533
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
Nonpolymer detailsNICKEL (NI): THERE IS AN ANOMALOUS SCATTERER ASSIGNED AS NI BRIDGING THE N-TERMINI OF THE A AND B CHAINS.

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 8.5
Details: 18% PEG MME2000, 0.16 M TRIS PH 8.5,0.01 M NI(II) CHLORIDE, 0.1 M MGCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9789
DetectorDate: Oct 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 4405 / % possible obs: 85.7 % / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 59.6
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6 / % possible all: 42.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0108refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BON (A 74-110, B)

1bon


Resolution: 2.27→41.72 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.836 / SU B: 34.725 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. THE GEOMETRY NEAR THE NI ATOM I ILL-DEFINED. HOWEVER THE PRESENCE OF NI IS CONFIRMED BY ANOMALOUS DIFFERENCE ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. THE GEOMETRY NEAR THE NI ATOM I ILL-DEFINED. HOWEVER THE PRESENCE OF NI IS CONFIRMED BY ANOMALOUS DIFFERENCE PATTERSONS. THE EXPERIMENTAL DATA IS NOT GOOD, AND THE R FACTOR HIGH. HOWEVER THE STRUCTURE REVEALS INTERESTING BIOCHEMICAL INSIGHTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.43475 173 4 %RANDOM
Rwork0.28341 ---
obs0.28921 4188 79.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.717 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å21.2 Å20 Å2
2--2.41 Å20 Å2
3----3.61 Å2
Refinement stepCycle: LAST / Resolution: 2.27→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms649 0 1 0 650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022665
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.81.934883
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.961575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.81423.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.83115134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.647156
X-RAY DIFFRACTIONr_chiral_restr0.0860.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02494
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.274→2.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.438 74 -
Rfree-0 -
obs--23.95 %
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)
11.3586-0.53070.3556.6961-0.259420.86240.09150.1068-0.1578-0.50310.1322-0.33870.77261.0681-0.22370.186-0.06820.00820.2465-0.03540.2008-1.5601-10.9375-12.262
25.7279-0.37971.895815.88925.03129.6667-0.01170.07920.1045-0.23720.3583-0.78160.22470.8547-0.34660.1730.04510.00310.34970.02980.0718-2.0253-13.8244-8.9055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A71 - 110
2X-RAY DIFFRACTION2B71 - 108

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