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- PDB-1l0o: Crystal Structure of the Bacillus stearothermophilus Anti-Sigma F... -

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Basic information

Entry
Database: PDB / ID: 1l0o
TitleCrystal Structure of the Bacillus stearothermophilus Anti-Sigma Factor SpoIIAB with the Sporulation Sigma Factor SigmaF
Components
  • Anti-sigma F factor
  • sigma factor
KeywordsPROTEIN BINDING / Bergerat fold / helix-turn-helix
Function / homology
Function and homology information


asexual sporulation / negative regulation of sporulation resulting in formation of a cellular spore / sigma factor antagonist activity / sporulation resulting in formation of a cellular spore / sigma factor activity / DNA-templated transcription initiation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / DNA binding / ATP binding
Similarity search - Function
RNA polymerase sigma-F type / RNA polymerase sigma-B/F/G type / Anti-sigma F factor / : / Histidine kinase-like ATPase domain / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Sigma-70 factors family signature 1. / : / RNA polymerase sigma-70 region 3 ...RNA polymerase sigma-F type / RNA polymerase sigma-B/F/G type / Anti-sigma F factor / : / Histidine kinase-like ATPase domain / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Sigma-70 factors family signature 1. / : / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Histidine kinase/HSP90-like ATPase superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Anti-sigma F factor / RNA polymerase sigma factor
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsCampbell, E.A. / Masuda, S. / Sun, J.L. / Muzzin, O. / Olson, C.A. / Wang, S. / Darst, S.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Crystal structure of the Bacillus stearothermophilus anti-sigma factor SpoIIAB with the sporulation sigma factor sigmaF.
Authors: Campbell, E.A. / Masuda, S. / Sun, J.L. / Muzzin, O. / Olson, C.A. / Wang, S. / Darst, S.A.
History
DepositionFeb 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-sigma F factor
B: Anti-sigma F factor
C: sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3757
Polymers61,4723
Non-polymers9034
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-50 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.31, 97.31, 262.98
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Anti-sigma F factor / SpoIIAB / Stage II sporulation protein AB


Mass: 16765.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: SpoIIAB / Production host: Escherichia coli (E. coli) / References: UniProt: O32727
#2: Protein sigma factor / SpoIIAC / sigma F


Mass: 27939.832 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-245 / Mutation: V233M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: O32728
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, ammonium sulfate, dioxane, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22.5 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl1droppH8.0
2200 mM1dropNaCl
310 mM1dropMgCl2
41 mMATP1drop
51 mMTCEP1drop
620 mg/mlprotein1drop
71.9 Mammonium sulfate1reservoir
8100 mMMES1reservoirpH6.0
910 %(v/v)dioxane1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. all: 17364 / Num. obs: 17312 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rsym value: 0.081 / Net I/σ(I): 30.8
Reflection shellResolution: 2.9→3.03 Å / Mean I/σ(I) obs: 6.4 / Rsym value: 0.31 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 35 Å / Num. measured all: 133526 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.307

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 1669 random
Rwork0.221 --
all0.221 16211 -
obs0.221 14542 -
Refinement stepCycle: LAST / Resolution: 2.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 56 83 2738
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0007
X-RAY DIFFRACTIONc_angle_deg0.2881
Refinement
*PLUS
Lowest resolution: 35 Å / % reflection Rfree: 10 % / Rfactor obs: 0.221 / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg0.288

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