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- PDB-1thn: Crystal Structures of the ADP and ATP bound forms of the Bacillus... -

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Basic information

Entry
Database: PDB / ID: 1thn
TitleCrystal Structures of the ADP and ATP bound forms of the Bacillus Anti-sigma factor SpoIIAB in complex with the Anti-anti-sigma SpoIIAA: inhibitory complex with ADP, crystal form I
Components
  • Anti-sigma F factor
  • Anti-sigma F factor antagonist
KeywordsTRANSCRIPTION / SpoIIAB / SpoIIAA / anti-sigma / anti-anti-sigma / sporulation / serine kinase
Function / homology
Function and homology information


asexual sporulation / negative regulation of sporulation resulting in formation of a cellular spore / anti-sigma factor antagonist activity / antisigma factor binding / sigma factor antagonist activity / sporulation resulting in formation of a cellular spore / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Anti-sigma F factor / : / Anti-sigma F factor antagonist / Histidine kinase-like ATPase domain / Anti-sigma factor antagonist / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain ...Anti-sigma F factor / : / Anti-sigma F factor antagonist / Histidine kinase-like ATPase domain / Anti-sigma factor antagonist / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DIMETHYLFORMAMIDE / Anti-sigma F factor antagonist / Anti-sigma F factor
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMasuda, S. / Murakami, K.S. / Wang, S. / Olson, C.A. / Donigan, J. / Leon, F. / Darst, S.A. / Campbell, E.A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structures of the ADP and ATP Bound Forms of the Bacillus Anti-sigma Factor SpoIIAB in Complex with the Anti-anti-sigma SpoIIAA.
Authors: Masuda, S. / Murakami, K.S. / Wang, S. / Olson, C.A. / Donigian, J. / Leon, F. / Darst, S.A. / Campbell, E.A.
History
DepositionJun 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model / 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_database_remark.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE DISCREPANCIES IN BOTH CHAINS ARE DUE TO STRAIN VARIATION.

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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 antagonist
C: Anti-sigma F factor
D: Anti-sigma F factor antagonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0927
Polymers58,1644
Non-polymers9273
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.056, 49.056, 265.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Detailsthe asymmetric unit contains one biological assembly of 2AB/2AA (a tetramer or 2 heterodimers)

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Components

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


Mass: 16266.276 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: SPOIIAB / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32727, EC: 2.7.1.37
#2: Protein Anti-sigma F factor antagonist / Stage II sporulation protein AA


Mass: 12815.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: SPOIIAA / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32726
#3: 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
#4: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 11
Details: 0.1M CAPS, 6% DMF, 2.0M lithium sulfate, pH 11, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 25532 / Num. obs: 25047 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.031 / Net I/σ(I): 39.56
Reflection shellResolution: 2.5→2.55 Å / Mean I/σ(I) obs: 11.27 / Num. unique all: 2497 / Rsym value: 0.11 / % possible all: 91.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry ID1L0O, pdb entry ID 1H4Y

1h4y


Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1252 -random
Rwork0.224 ---
obs-24658 98.1 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 59 53 4004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00917
X-RAY DIFFRACTIONc_angle_d1.48896

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