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- PDB-1h4y: Structure of the Anti-Sigma Factor Antagonist SpoIIAA in its Unph... -

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Basic information

Entry
Database: PDB / ID: 1h4y
TitleStructure of the Anti-Sigma Factor Antagonist SpoIIAA in its Unphosphorylated Form
ComponentsANTI-SIGMA F FACTOR ANTAGONIST
KeywordsCELL DIFFERENTIATION / PHOSPHORYLATION / SIGMA FACTORS / SPORULATION
Function / homology
Function and homology information


anti-sigma factor antagonist activity / antisigma factor binding / sporulation resulting in formation of a cellular spore
Similarity search - Function
Anti-sigma F factor antagonist / Anti-sigma factor antagonist / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Anti-sigma F factor antagonist
Similarity search - Component
Biological speciesBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.61 Å
AuthorsSeavers, P.R. / Lewis, R.J. / Brannigan, J.A. / Verschueren, K.H.G. / Murshudov, G.N. / Wilkinson, A.J.
CitationJournal: Structure / Year: 2001
Title: Structure of the Bacillus Cell Fate Determinant Spoiiaa in Phosphorylated and Unphosphorylated Forms
Authors: Seavers, P.R. / Lewis, R.J. / Brannigan, J.A. / Verschueren, K.H.G. / Murshudov, G.N. / Wilkinson, A.J.
History
DepositionMay 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: ANTI-SIGMA F FACTOR ANTAGONIST
B: ANTI-SIGMA F FACTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)26,1862
Polymers26,1862
Non-polymers00
Water3,711206
1
A: ANTI-SIGMA F FACTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)13,0931
Polymers13,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ANTI-SIGMA F FACTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)13,0931
Polymers13,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.764, 53.543, 101.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANTI-SIGMA F FACTOR ANTAGONIST / SPOIIAA


Mass: 13093.158 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SPHAERICUS (bacteria) / Strain: ATCC14577 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: O32723*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION MET86VAL IN THE PHOSPHORYLATED FORM COUNTERACTS SPOIIAB THUS RELEASING SIGMA F
Sequence detailsTHE SEQUENCE SPOIIA FROM BACILLUS SPHAERICUSS STRAIN ATCC14577, IS SIMILAR TO THE SWISSPROT ENTRY ...THE SEQUENCE SPOIIA FROM BACILLUS SPHAERICUSS STRAIN ATCC14577, IS SIMILAR TO THE SWISSPROT ENTRY O32723: 1H4X AFQLEMVTRETVVIRLFGELDHHAVEQIRAKISTAIF O32723 MHFQLEMVTRETVVIRLFGELDHHAVEQIRAKISAAIF 1H4X QGAVTTIIWNFERLSFMDSSGVGLVLGRMRELEAVAGR O32723 QGTVTTIIWNLEGLSFMDSSGVGLVLGRMRELEAVAGR 1H4X TILLNPSPTMRKVFQFSGLGPWMMDATEEEAIDRVR O32723 TILLNPSPTMRKVFQFSGLGPWMMDATEEQAIDRVRGIVNG THE SEQUENCE FOR THE PROTEIN FROM STRAIN ATCC14577 HAS NOT BEEN DEPOSITED.

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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: 1.9 Å3/Da / Density % sol: 35.41 %
Description: ABOVE DATA IS THE NATIVE DATA TO 1.61A. THE STRUCTURE WAS ORIGINALLY SOLVED BY MAD TO 2.5A.
Crystal growpH: 8.5 / Details: 15% PEG 4K, 200MM MGCL2, 0.1M TRIS (PH 8.5)
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Seavers, P.R., (2001) Acta Crystallogr., D57, 292.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNaCl
41 mMdithiothreitol1drop
515 %PEG40001reservoir
6200 mM1reservoirMgCl2
7100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.61→19.9 Å / Num. obs: 25927 / % possible obs: 96.4 % / Redundancy: 4.57 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.8
Reflection shellResolution: 1.61→1.67 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.4 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 118510
Reflection shell
*PLUS
% possible obs: 87.1 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.61→20 Å / SU B: 4.912 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.1 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.214 -5.8 %RANDOM
Rwork0.159 ---
obs-24554 96.4 %-
Refinement stepCycle: LAST / Resolution: 1.61→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 206 2018
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.801
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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