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- PDB-1b0n: SINR PROTEIN/SINI PROTEIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1b0n
TitleSINR PROTEIN/SINI PROTEIN COMPLEX
Components
  • PROTEIN (SINI PROTEIN)
  • PROTEIN (SINR PROTEIN)
KeywordsTRANSCRIPTION 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. / 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
HTH-type transcriptional regulator SinR / Protein SinI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsLewis, R.J. / Brannigan, J.A. / Offen, W.A. / Smith, I. / Wilkinson, A.J.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: An evolutionary link between sporulation and prophage induction in the structure of a repressor:anti-repressor complex.
Authors: Lewis, R.J. / Brannigan, J.A. / Offen, W.A. / Smith, I. / Wilkinson, A.J.
History
DepositionNov 11, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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: PROTEIN (SINR PROTEIN)
B: PROTEIN (SINI PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9497
Polymers19,6222
Non-polymers3275
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-157 kcal/mol
Surface area7790 Å2
MethodPISA
2
A: PROTEIN (SINR PROTEIN)
B: PROTEIN (SINI PROTEIN)
hetero molecules

A: PROTEIN (SINR PROTEIN)
B: PROTEIN (SINI PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,89814
Polymers39,2444
Non-polymers65410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9080 Å2
ΔGint-369 kcal/mol
Surface area13870 Å2
MethodPISA
3
A: PROTEIN (SINR PROTEIN)
B: PROTEIN (SINI PROTEIN)
hetero molecules

A: PROTEIN (SINR PROTEIN)
B: PROTEIN (SINI PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,89814
Polymers39,2444
Non-polymers65410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area9710 Å2
ΔGint-361 kcal/mol
Surface area13240 Å2
MethodPISA
4
A: PROTEIN (SINR PROTEIN)
hetero molecules

A: PROTEIN (SINR PROTEIN)
hetero molecules

B: PROTEIN (SINI PROTEIN)

B: PROTEIN (SINI PROTEIN)


Theoretical massNumber of molelcules
Total (without water)39,89814
Polymers39,2444
Non-polymers65410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
crystal symmetry operation2_665-y+1,x-y+1,z+1/31
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Buried area3700 Å2
ΔGint-265 kcal/mol
Surface area19250 Å2
MethodPISA
5
A: PROTEIN (SINR PROTEIN)
hetero molecules

A: PROTEIN (SINR PROTEIN)
hetero molecules

B: PROTEIN (SINI PROTEIN)

B: PROTEIN (SINI PROTEIN)


Theoretical massNumber of molelcules
Total (without water)39,89814
Polymers39,2444
Non-polymers65410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation2_665-y+1,x-y+1,z+1/31
crystal symmetry operation5_665x-y+1,-y+1,-z+2/31
Buried area2600 Å2
ΔGint-251 kcal/mol
Surface area20350 Å2
MethodPISA
6
A: PROTEIN (SINR PROTEIN)
hetero molecules

A: PROTEIN (SINR PROTEIN)
hetero molecules

B: PROTEIN (SINI PROTEIN)

B: PROTEIN (SINI PROTEIN)


Theoretical massNumber of molelcules
Total (without water)39,89814
Polymers39,2444
Non-polymers65410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
crystal symmetry operation3_674-x+y+1,-x+2,z-1/31
crystal symmetry operation4_556y,x,-z+11
Buried area3460 Å2
ΔGint-262 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.900, 60.900, 87.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN (SINR PROTEIN)


Mass: 13009.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cellular location: CYTOPLASM / Gene: SINR, SINI / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06533
#2: Protein PROTEIN (SINI PROTEIN)


Mass: 6612.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cellular location: CYTOPLASM / Gene: SINR, SINI / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P23308
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1300 mMzinc acetate1reservoir
250 mMMES1reservoir
31-4 %mPEG20001reservoir
4200 mMsodium chloride1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 15070 / % possible obs: 98.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.039 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.149 / % possible all: 94.7
Reflection
*PLUS
Num. measured all: 45969 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 94.7 % / Rmerge(I) obs: 0.149

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
Agrovatadata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 759 5 %RANDOM
Rwork0.199 ---
obs-15150 98.7 %-
Displacement parametersBiso mean: 28.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 5 117 1234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8592
X-RAY DIFFRACTIONp_mcangle_it3.5763
X-RAY DIFFRACTIONp_scbond_it4.0342
X-RAY DIFFRACTIONp_scangle_it5.8163
X-RAY DIFFRACTIONp_plane_restr0.0210.03
X-RAY DIFFRACTIONp_chiral_restr0.1310.15
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1240.3
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.220
X-RAY DIFFRACTIONp_special_tor

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