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- PDB-1h4z: Structure of the Anti-Sigma Factor Antagonist SpoIIAA in its Unph... -

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Basic information

Entry
Database: PDB / ID: 1h4z
TitleStructure of the Anti-Sigma Factor Antagonist SpoIIAA in its Unphosphorylated Form
ComponentsANTI-SIGMA F FACTOR ANTAGONIST
KeywordsCELL DIFFERENTIATION / PHOSPHORYLATION / SIGMA FACTOR / 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 / MOLECULAR REPLACEMENT / Resolution: 2.74 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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


Theoretical massNumber of molelcules
Total (without water)13,1251
Polymers13,1251
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.582, 81.582, 71.616
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 13125.223 Da / Num. of mol.: 1
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): BL21 / References: UniProt: O32723*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growpH: 9 / Details: 2M MGCL2, 0.1M BICINE (PH 9.0)
Crystal grow
*PLUS
Temperature: 291 K / pH: 8.5 / 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: ID14-3 / Wavelength: 0.93
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.74→20 Å / Num. obs: 4022 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.5
Reflection shellResolution: 2.74→2.84 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 5.3 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 26991
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H4X

1h4x


Resolution: 2.74→20 Å / SU B: 14.33 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 1.068 / ESU R Free: 0.404 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.305 181 4.5 %RANDOM
Rwork0.251 ---
obs-3811 99.85 %-
Refinement stepCycle: LAST / Resolution: 2.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 0 8 881
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.25 / Rfactor Rfree: 0.305 / Rfactor Rwork: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d2.021

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