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- PDB-5mqh: Structure of the Phosphatase Domain of the Cell Fate Determinant ... -

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Basic information

Entry
Database: PDB / ID: 5mqh
TitleStructure of the Phosphatase Domain of the Cell Fate Determinant SpoIIE from Bacillus subtilis in a crystal form without domain swapping
ComponentsSerine phosphatase
KeywordsTRANSFERASE / Sporulation / Phosphatase / PP2C / Manganese
Function / homology
Function and homology information


endospore-forming forespore / sporulation resulting in formation of a cellular spore / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphatase activity / membrane / plasma membrane
Similarity search - Function
Stage II sporulation protein E / Stage II sporulation protein E, N-terminal / Stage II sporulation protein E N-terminal / : / Stage II sporulation protein E (SpoIIE) / Sigma factor PP2C-like phosphatases / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily
Similarity search - Domain/homology
Serine phosphatase / Stage II sporulation protein E
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLevdikov, V.M. / Wilkinson, A.J. / Blagova, E.V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust082829 United Kingdom
Citation
Journal: Elife / Year: 2017
Title: A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases.
Authors: Bradshaw, N. / Levdikov, V.M. / Zimanyi, C.M. / Gaudet, R. / Wilkinson, A.J. / Losick, R.
#1: Journal: J. Mol. Biol. / Year: 2012
Title: Structure of the phosphatase domain of the cell fate determinant SpoIIE from Bacillus subtilis.
Authors: Levdikov, V.M. / Blagova, E.V. / Rawlings, A.E. / Jameson, K. / Tunaley, J. / Hart, D.J. / Barak, I. / Wilkinson, A.J.
#2: Journal: Elife / Year: 2015
Title: Asymmetric division triggers cell-specific gene expression through coupled capture and stabilization of a phosphatase.
Authors: Bradshaw, N. / Losick, R.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine phosphatase


Theoretical massNumber of molelcules
Total (without water)27,4171
Polymers27,4171
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.285, 122.506, 81.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-633-

GLY

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Components

#1: Protein Serine phosphatase


Mass: 27417.348 Da / Num. of mol.: 1 / Mutation: A624I
Source method: isolated from a genetically manipulated source
Details: The mutation Ala624 to Ile was introduced to reduce successfully the extent of domain swapping.
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SC09_Contig28orf00413 / Plasmid: pETYSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D1KMY9, UniProt: P37475*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2M Sodium formate, 0.1M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.44→61.34 Å / Num. obs: 10961 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rsym value: 0.057 / Net I/σ(I): 20.1
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.8 / CC1/2: 0.874 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T9L

3t9l


Resolution: 2.45→48.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.871 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.29 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27751 512 4.8 %RANDOM
Rwork0.21055 ---
obs0.21386 10188 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.958 Å2
Baniso -1Baniso -2Baniso -3
1--4.16 Å2-0 Å20 Å2
2--3.07 Å2-0 Å2
3---1.09 Å2
Refinement stepCycle: 1 / Resolution: 2.45→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 0 33 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191780
X-RAY DIFFRACTIONr_bond_other_d0.0020.021705
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9682398
X-RAY DIFFRACTIONr_angle_other_deg0.99133969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5155226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93225.20573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.0115337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.432158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021948
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02320
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5016.498910
X-RAY DIFFRACTIONr_mcbond_other4.4336.492909
X-RAY DIFFRACTIONr_mcangle_it6.9199.7191134
X-RAY DIFFRACTIONr_mcangle_other6.9229.7291135
X-RAY DIFFRACTIONr_scbond_it5.3177.171869
X-RAY DIFFRACTIONr_scbond_other5.3147.18870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.44810.5081265
X-RAY DIFFRACTIONr_long_range_B_refined10.97377.4471917
X-RAY DIFFRACTIONr_long_range_B_other10.97877.3981915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 41 -
Rwork0.402 722 -
obs--99.74 %

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