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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
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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


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