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- PDB-3w44: Crystal structure of RsbX, selenomethionine derivative -

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Basic information

Entry
Database: PDB / ID: 3w44
TitleCrystal structure of RsbX, selenomethionine derivative
ComponentsPhosphoserine phosphatase RsbX
KeywordsHYDROLASE / Signaling protein / Gene Expression Regulation / Stressosome / Environmental stress / Phosphoric Monoester Hydrolases / Dephosphorylation / Protein Structure / Tertiary / phosphatase / Hydrolase Protein phosphatase / magnesium/manganese binding
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / phosphoprotein phosphatase activity / response to heat
Similarity search - Function
Phosphatase RsbX / 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
: / DI(HYDROXYETHYL)ETHER / Phosphoserine phosphatase RsbX
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.3 Å
AuthorsTeh, A.H. / Makino, M. / Baba, S. / Shimizu, N. / Yamamoto, M. / Kumasaka, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the RsbX phosphatase involved in the general stress response of Bacillus subtilis
Authors: Teh, A.H. / Makino, M. / Hoshino, T. / Baba, S. / Shimizu, N. / Yamamoto, M. / Kumasaka, T.
History
DepositionJan 4, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoserine phosphatase RsbX
B: Phosphoserine phosphatase RsbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0457
Polymers44,7192
Non-polymers3265
Water4,576254
1
A: Phosphoserine phosphatase RsbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4693
Polymers22,3601
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoserine phosphatase RsbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5764
Polymers22,3601
Non-polymers2163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.610, 85.610, 103.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 199
2115B1 - 199

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Components

#1: Protein Phosphoserine phosphatase RsbX / Sigma-B negative effector


Mass: 22359.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU04740, rsbX / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P17906, phosphoserine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 27% PEG 4000, 90mM Tris-HCl, 0.18M MgCl2, 0.12M MnCl2, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.978 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 6, 2009 / Details: Toroidal Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionRedundancy: 14.3 % / Rmerge(I) obs: 0.091 / Χ2: 0.97 / D res high: 2.4 Å / D res low: 50 Å
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.175010.0531.14213.1
4.15.1710.0480.9114.2
3.584.110.0570.84714.4
3.263.5810.0720.86414.5
3.023.2610.0980.98414.6
2.853.0210.1561.03314.7
2.72.8510.1951.0214.7
2.592.710.2560.98814.7
2.492.5910.3560.96714.6
2.42.4910.4120.9813.8
ReflectionResolution: 2.2→50 Å / Num. obs: 19928 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.089 / Net I/σ(I): 13.64
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.57 / Rsym value: 0.422 / % possible all: 87.4

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Phasing

PhasingMethod: MAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 13881
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.94-10023.80.848503
6.23-7.9424.30.886507
5.4-6.2321.30.913503
4.88-5.418.70.926508
4.51-4.8819.40.929510
4.24-4.5117.40.926505
4.01-4.2416.10.932505
3.83-4.0117.10.917504
3.68-3.8316.30.924506
3.54-3.6816.70.925505
3.43-3.5416.40.926517
3.32-3.4317.90.934521
3.23-3.3219.80.928538
3.14-3.2322.90.928546
3.06-3.14200.933564
2.98-3.0622.60.912585
2.91-2.9823.80.911586
2.85-2.9122.30.906600
2.79-2.8526.10.898616
2.73-2.7924.20.887630
2.68-2.7323.80.903617
2.63-2.6827.70.9657
2.58-2.63310.852665
2.5-2.5833.80.8241183

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Processing

Software
NameVersionClassificationNB
SOLVE2.13phasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 16.095 / SU ML: 0.176 / SU R Cruickshank DPI: 0.4487 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.253
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.24036 897 5.1 %RANDOM
Rwork0.18783 ---
obs0.19052 16847 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.917 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 11 254 3373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223192
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.9674298
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6595403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.24625.379145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5215598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0961512
X-RAY DIFFRACTIONr_chiral_restr0.1180.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212376
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1141.51984
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.22223200
X-RAY DIFFRACTIONr_scbond_it3.79131208
X-RAY DIFFRACTIONr_scangle_it6.294.51094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
792MEDIUM POSITIONAL0.20.5
739LOOSE POSITIONAL0.555
792MEDIUM THERMAL2.052
739LOOSE THERMAL2.8710
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 76 -
Rwork0.21 1193 -
obs--99.37 %
Refinement TLS params.Method: refined / Origin x: 22.4699 Å / Origin y: 21.5636 Å / Origin z: 52.0045 Å
111213212223313233
T0.0101 Å2-0.0063 Å20.0118 Å2-0.0078 Å2-0.0037 Å2--0.0489 Å2
L0.279 °20.0202 °20.3384 °2-0.3575 °2-0.3231 °2--2.0365 °2
S-0.0004 Å °0.0071 Å °0.0006 Å °-0.0079 Å °0.0401 Å °0.002 Å °0.093 Å °-0.0867 Å °-0.0397 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 199
2X-RAY DIFFRACTION1B1 - 199

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