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- PDB-3t91: Structure of the Phosphatase Domain of the Cell Fate Determinant ... -

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Basic information

Entry
Database: PDB / ID: 3t91
TitleStructure of the Phosphatase Domain of the Cell Fate Determinant SpoIIE from Bacillus subtilis
ComponentsStage II sporulation protein E
KeywordsHYDROLASE / SpoIIE / phosphatase / sporulation / manganese binding / PP2C Phosphatase Domain / dephosphorylating the anti-sigma factor antagonist SpoIIAA
Function / homology
Function and homology information


endospore-forming forespore / myosin phosphatase activity / sporulation resulting in formation of a cellular spore / protein-serine/threonine phosphatase / 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 / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain ...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 / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-gulopyranose / alpha-D-mannopyranose / : / Stage II sporulation protein E
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å
AuthorsLevdikov, V.M. / Blagova, E.V. / Wilkinson, A.J.
CitationJournal: 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.
History
DepositionAug 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stage II sporulation protein E
B: Stage II sporulation protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5516
Polymers53,0812
Non-polymers4704
Water2,882160
1
A: Stage II sporulation protein E
B: Stage II sporulation protein E
hetero molecules

A: Stage II sporulation protein E
B: Stage II sporulation protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,10212
Polymers106,1624
Non-polymers9408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area21650 Å2
ΔGint-116 kcal/mol
Surface area38400 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-47 kcal/mol
Surface area20420 Å2
MethodPISA
3
A: Stage II sporulation protein E
hetero molecules

B: Stage II sporulation protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5516
Polymers53,0812
Non-polymers4704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area1450 Å2
ΔGint-18 kcal/mol
Surface area28570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.618, 87.618, 321.597
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Stage II sporulation protein E / Stage II sporulation protein H


Mass: 26540.422 Da / Num. of mol.: 2 / Fragment: unp residues 590-827
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU00640, spoIIE, spoIIH / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P37475, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Sugar ChemComp-GL0 / beta-D-gulopyranose / beta-D-gulose / D-gulose / gulose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGulpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-gulopyranoseCOMMON NAMEGMML 1.0
b-D-GulpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GulSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12 - 15% PEG 4000, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2009 / Details: torodial focusing mirror
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. all: 23618 / Num. obs: 23618 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 79.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 30.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1129 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.64→10 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 23.152 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27891 1184 5.2 %RANDOM
Rwork0.22015 ---
all0.22306 21784 --
obs0.22306 21784 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.776 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å21.26 Å20 Å2
2--2.52 Å20 Å2
3----3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.64→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 26 160 3498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223471
X-RAY DIFFRACTIONr_bond_other_d0.0020.022365
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.984678
X-RAY DIFFRACTIONr_angle_other_deg0.84335817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7325441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35225.035141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.78915669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9081519
X-RAY DIFFRACTIONr_chiral_restr0.0740.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023781
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02626
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_it2.01352182
X-RAY DIFFRACTIONr_mcbond_other0.4495899
X-RAY DIFFRACTIONr_mcangle_it3.64673527
X-RAY DIFFRACTIONr_scbond_it5.40391289
X-RAY DIFFRACTIONr_scangle_it8.65201150
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 69 -
Rwork0.415 1494 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.33430.19220.23341.1884-0.30261.56830.019-0.1317-0.16440.017-0.00630.03390.06310.0241-0.01260.00510.0041-0.00480.06290.00550.0361-5.443-35.077-4.243
226.67357.4078-2.70882.0591-0.75340.2787-0.38440.8184-0.9691-0.11360.2556-0.27070.0437-0.09340.12880.53550.03190.06790.52310.02670.329810.9-28.087-15.925
37.60765.6667-3.27254.2282-2.4391.41430.0629-0.3236-0.19570.0294-0.1964-0.1233-0.00860.10760.13350.51660.11670.03380.543-0.07290.5292-29.941-17.283-13.882
44.46525.7082-1.46027.3255-1.8750.4860.4291-0.2895-0.09550.6265-0.4618-0.0977-0.2040.08830.03280.60320.0215-0.08590.5987-0.09410.6159-26.073-26.939-21.756
58.3652-1.33854.36660.3832-1.83639.9848-0.2427-0.29930.2470.13810.0539-0.0327-0.7292-0.18340.18890.2765-0.0450.03620.13870.02720.3679-20.19-52.537-2.131
65.1042-2.69111.50771.4386-0.55084.79690.24670.02580.7344-0.17480.0126-0.4293-0.0487-0.0256-0.25930.4234-0.03930.01960.3689-0.02440.4303-5.879-52.539-17.629
72.6239-1.8599-5.64381.33784.043712.24310.07390.4469-0.08820.0448-0.34320.08380.0615-1.02930.26930.61190.0116-0.01670.49450.01370.5866-13.419-56.1094.84
86.6001-5.0174-1.58995.21864.17196.6433-0.05670.19720.56750.18180.1722-0.39590.31070.611-0.11540.3599-0.05580.00220.27790.06070.5095-18.667-11.539-4.622
90.7453-0.11310.47090.7033-0.55352.03550.04720.08190.1835-0.1428-0.0766-0.0395-0.15550.1130.02950.1030.01960.00270.0608-0.00420.1111-7.465-21.775-22.852
1071.1347-27.18928.114836.5823-28.356622.98120.6102-1.5271.61471.2854-1.0589-0.4193-0.81020.4330.44870.38820.11260.1010.4417-0.00290.3008-22.597-21.265-3.22
119.37381.04479.40749.2715-1.846510.3624-0.28160.1446-0.08360.36910.2702-0.2013-0.42040.03710.01140.2724-0.04040.0290.4092-0.09570.318311.702-38.672-14.994
121.45192.629-1.93884.7662-3.50962.59030.018-0.0686-0.11990.0613-0.1616-0.2318-0.03630.07990.14360.50150.0666-0.04240.502-0.09040.4730.695-45.729-18.234
136.3232.05793.32950.68841.07631.75830.0093-0.08480.17580.0152-0.1144-0.0095-0.0029-0.00020.1050.391-0.03070.00060.50180.18780.4075-6.131-23.151-43.01
142.29951.0645-0.21270.5102-0.10020.02040.0065-0.04530.3522-0.07150.01720.21730.0117-0.0062-0.02370.59040.0684-0.02660.52410.05240.5975-25.937-27.671-32.094
150.1105-0.53540.08253.6252-0.9220.35640.04180.07580.0380.33720.0280.1667-0.3101-0.1519-0.06990.58310.07730.03490.48140.04550.47-14.827-2.059-21.354
160.01980.0985-0.05990.5556-0.32080.1947-0.01040.03210.09510.02230.27850.47540.0257-0.156-0.2680.49410.06930.01330.42030.020.5807-23.533-5.237-13.9
170.5103-2.5377-2.345514.181513.123612.24470.41420.02710.1137-1.48050.0599-0.6723-1.4047-0.0641-0.47410.51040.0487-0.06110.33780.02720.35187.891-21.002-14.111
189.7438-6.3467-3.49234.13782.344711.64740.455-0.4613-0.0301-0.32480.2870.0179-0.59670.3864-0.74190.3703-0.09650.13110.4017-0.03020.553526.934-38.164-10.836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A590 - 600
2X-RAY DIFFRACTION1A610 - 628
3X-RAY DIFFRACTION1A636 - 654
4X-RAY DIFFRACTION1A663 - 669
5X-RAY DIFFRACTION1A679 - 715
6X-RAY DIFFRACTION1A724 - 806
7X-RAY DIFFRACTION2A588 - 589
8X-RAY DIFFRACTION3A601 - 609
9X-RAY DIFFRACTION4A629 - 635
10X-RAY DIFFRACTION5A655 - 662
11X-RAY DIFFRACTION6A670 - 678
12X-RAY DIFFRACTION7A716 - 723
13X-RAY DIFFRACTION8A807 - 811
14X-RAY DIFFRACTION9B591 - 601
15X-RAY DIFFRACTION9B609 - 628
16X-RAY DIFFRACTION9B636 - 653
17X-RAY DIFFRACTION9B659 - 668
18X-RAY DIFFRACTION9B679 - 745
19X-RAY DIFFRACTION9B771 - 782
20X-RAY DIFFRACTION9B797 - 805
21X-RAY DIFFRACTION9B808 - 815
22X-RAY DIFFRACTION10B589 - 590
23X-RAY DIFFRACTION11B602 - 608
24X-RAY DIFFRACTION12B629 - 635
25X-RAY DIFFRACTION13B654 - 658
26X-RAY DIFFRACTION14B669 - 678
27X-RAY DIFFRACTION15B746 - 770
28X-RAY DIFFRACTION16B783 - 796
29X-RAY DIFFRACTION17B806 - 807
30X-RAY DIFFRACTION18B816 - 819

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