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- PDB-1h4x: Structure of the Bacillus Cell Fate Determinant SpoIIAA in the Ph... -

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Basic information

Entry
Database: PDB / ID: 1h4x
TitleStructure of the Bacillus Cell Fate Determinant SpoIIAA in the Phosphorylated 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: 1.16 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 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTI-SIGMA F FACTOR ANTAGONIST
B: ANTI-SIGMA F FACTOR ANTAGONIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6554
Polymers26,4102
Non-polymers2442
Water7,674426
1
A: ANTI-SIGMA F FACTOR ANTAGONIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3272
Polymers13,2051
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ANTI-SIGMA F FACTOR ANTAGONIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3272
Polymers13,2051
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.119, 61.577, 65.892
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: 13205.202 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SPHAERICUS (bacteria) / Strain: ATCC14577 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O32723*PLUS
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN 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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growpH: 6.5
Details: 30% PEG 5K MME, 200MM (NH4)2SO4, 100MM MES (PH 6.5)
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: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.16→20 Å / Num. obs: 72227 / % possible obs: 97.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.9
Reflection shellResolution: 1.16→1.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.72 / % possible all: 85.4
Reflection
*PLUS
Num. measured all: 277544
Reflection shell
*PLUS
% possible obs: 85.4 % / Rmerge(I) obs: 0.3

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→19.61 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.218 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.164 3626 5.1 %RANDOM
Rwork0.133 ---
obs-68102 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 1.16→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 16 426 2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221857
X-RAY DIFFRACTIONr_bond_other_d0.0010.021794
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.0861.962516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.92234140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1290.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021960
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02385
X-RAY DIFFRACTIONr_nbd_refined0.2680.3424
X-RAY DIFFRACTIONr_nbd_other0.2450.31764
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other1.0470.55
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2590.5258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.371
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.577
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8341.51118
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.66621833
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3953739
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7384.5683
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.212 231
Rwork0.181 4628
Software
*PLUS
Name: REFMAC / Version: 5.0.36 18/01/2001 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.133 / Rfactor Rfree: 0.164 / Rfactor Rwork: 0.133
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.025
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.921

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