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- PDB-5ucg: Structure of the PP2C Phosphatase Domain and a Fragment of the Re... -

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Basic information

Entry
Database: PDB / ID: 5ucg
TitleStructure of the PP2C Phosphatase Domain and a Fragment of the Regulatory Domain of the Cell Fate Determinant SpoIIE from Bacillus Subtilis
ComponentsStage II sporulation protein E
KeywordsHYDROLASE / PPM Phosphatase
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 / 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
Stage II sporulation protein E
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.906 Å
AuthorsBradshaw, N. / Levdikov, V. / Zimanyi, C. / Gaudet, R. / Wilkinson, A. / Losick, R.
Funding support United States, United Kingdom, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM18568 United States
Wellcome Trust082829 United Kingdom
Damon Runyon Cancer Research FoundationDRG 2051-10 United States
Jane Coffin Childs Memorial Fund for Medical ResearchJCC Fund United States
CitationJournal: 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.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
E: Stage II sporulation protein E
B: Stage II sporulation protein E
C: Stage II sporulation protein E
D: Stage II sporulation protein E


Theoretical massNumber of molelcules
Total (without water)192,1445
Polymers192,1445
Non-polymers00
Water0
1
A: Stage II sporulation protein E
B: Stage II sporulation protein E


Theoretical massNumber of molelcules
Total (without water)76,8572
Polymers76,8572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-20 kcal/mol
Surface area35350 Å2
MethodPISA
2
E: Stage II sporulation protein E

E: Stage II sporulation protein E


Theoretical massNumber of molelcules
Total (without water)76,8572
Polymers76,8572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3940 Å2
ΔGint-14 kcal/mol
Surface area34430 Å2
MethodPISA
3
C: Stage II sporulation protein E
D: Stage II sporulation protein E


Theoretical massNumber of molelcules
Total (without water)76,8572
Polymers76,8572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-17 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.622, 125.622, 330.696
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 38428.723 Da / Num. of mol.: 5 / Fragment: residues 465-809
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: spoIIE, spoIIH, BSU00640 / Plasmid: pET47B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: P37475, protein-serine/threonine phosphatase

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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: 3.39 Å3/Da / Density % sol: 63.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.5 mM LiSO4, 8% PEG8000, 0.05 mM NaF, 6% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.9→60 Å / Num. obs: 24917 / % possible obs: 99.7 % / Redundancy: 11.4 % / Biso Wilson estimate: 42.46 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.031 / Rrim(I) all: 0.107 / Χ2: 0.97 / Net I/σ(I): 4.3 / Num. measured all: 284918
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.9-3.976.81.44811810.8470.5631.5630.99297.4
3.97-4.047.31.22212180.7360.4651.3140.99998.2
4.04-4.127.81.05511930.6760.3881.1291.00699.2
4.12-4.29.21.07112250.7350.3651.1350.987100
4.2-4.2910.60.90312060.850.2870.9490.98399.9
4.29-4.3911.30.83612130.8760.2570.8751.00299.8
4.39-4.5120.66712410.9240.1990.6971.001100
4.5-4.6212.60.5312220.9630.1550.5531.021100
4.62-4.7612.90.4612310.9640.1320.4781.029100
4.76-4.9113.10.37112300.9790.1060.3861.04299.9
4.91-5.0912.80.30712290.9820.0890.321.00299.9
5.09-5.2912.30.29712450.9850.0870.311.005100
5.29-5.5311.40.26812400.9860.0820.2810.997100
5.53-5.8213.40.25512330.9870.0720.2651.011100
5.82-6.1913.40.23112610.9910.0650.240.967100
6.19-6.6713.10.16612700.9940.0470.1730.982100
6.67-7.3412.70.10312690.9960.030.1080.948100
7.34-8.411.30.0612800.9980.0190.0630.888100
8.4-10.5712.90.03913150.9990.0110.0410.82199.9
10.57-6011.20.03114150.9990.0090.0330.78399.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T91

3t91


Resolution: 3.906→50.054 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3225 1091 5.06 %
Rwork0.2762 20467 -
obs0.2786 21558 86.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.68 Å2 / Biso mean: 93.255 Å2 / Biso min: 19.94 Å2
Refinement stepCycle: final / Resolution: 3.906→50.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13166 0 0 0 13166
Num. residues----1685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213340
X-RAY DIFFRACTIONf_angle_d0.52517928
X-RAY DIFFRACTIONf_chiral_restr0.0432055
X-RAY DIFFRACTIONf_plane_restr0.0022319
X-RAY DIFFRACTIONf_dihedral_angle_d15.8758224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9061-4.08380.3014520.29591013106535
4.0838-4.2990.3817950.28681732182760
4.299-4.56820.32721650.28072751291695
4.5682-4.92060.32551610.255529053066100
4.9206-5.41530.30621510.265729303081100
5.4153-6.19760.35521610.328529463107100
6.1976-7.80360.36121560.317830143170100
7.8036-50.05820.27111500.237231763326100
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)
12.08010.2901-0.25121.32720.51181.02790.3570.33360.2761-0.6231-0.1405-0.1782-0.00350.6145-0.190.88050.28270.1380.86120.07360.416465.0887-57.5885-26.2392
21.4380.7442-0.82012.57970.33472.9035-0.01020.21060.253-0.3512-0.06290.5421-0.1668-0.83380.1970.51780.16010.0290.5561-0.19090.138650.5136-47.8654-1.7844
30.27630.01480.13941.0136-0.06190.6144-0.17940.16620.0058-0.05950.0634-0.4453-0.36420.59940.20030.7393-0.5268-0.37841.20290.33360.83918.9878-3.784816.6143
42.08371.17810.62371.37410.04872.7093-0.54310.50930.7121-0.29620.4520.5228-0.8496-0.1294-0.22770.4862-0.2607-0.09040.63950.3010.2054-10.2808-8.035820.8578
51.56760.309-0.21490.64710.02730.37120.12321.04150.0435-0.5798-0.0010.335-0.3066-0.256-0.09611.21820.1338-0.51111.1893-0.11920.812820.075-58.7846-32.9643
60.21040.3766-0.26891.1803-1.02612.7446-0.06310.0805-0.8097-0.0060.0161-0.4303-0.01760.57520.02871.00460.0334-0.46690.462-0.15361.322925.1878-78.0828-15.3939
70.34410.4972-0.2411.15630.06651.0185-0.02680.0387-0.3851-0.02150.07690.21520.6881-0.417-0.06320.8701-0.2223-0.42140.723-0.01191.7606-2.6701-75.39624.1754
81.21630.9006-1.48742.233-0.82732.72620.31120.2130.23520.1607-0.20821.0456-0.5492-0.702-0.0221.007-0.0261-0.54110.7149-0.0951.3127-6.6656-53.4471-11.596
90.86560.06840.15410.1052-0.02510.81260.1521-0.546-0.270.27240.06010.61140.3513-0.66-0.1660.7772-0.11830.21571.03860.4811.0046-15.6551-40.263432.8598
103.19770.6579-0.13331.2896-1.88183.58790.22850.3355-0.8709-0.5232-0.1655-0.24981.09440.515-0.46530.43180.0846-0.29450.51530.26730.583712.7854-37.711922.1703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 465 through 591 )A465 - 591
2X-RAY DIFFRACTION2chain 'A' and (resid 592 through 809 )A592 - 809
3X-RAY DIFFRACTION3chain 'E' and (resid 467 through 591 )E467 - 591
4X-RAY DIFFRACTION4chain 'E' and (resid 592 through 809 )E592 - 809
5X-RAY DIFFRACTION5chain 'B' and (resid 465 through 610 )B465 - 610
6X-RAY DIFFRACTION6chain 'B' and (resid 611 through 804 )B611 - 804
7X-RAY DIFFRACTION7chain 'C' and (resid 469 through 610 )C469 - 610
8X-RAY DIFFRACTION8chain 'C' and (resid 611 through 807 )C611 - 807
9X-RAY DIFFRACTION9chain 'D' and (resid 469 through 591 )D469 - 591
10X-RAY DIFFRACTION10chain 'D' and (resid 592 through 808 )D592 - 808

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