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- PDB-3w40: Crystal structure of RsbX in complex with magnesium in space group P1 -

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Basic information

Entry
Database: PDB / ID: 3w40
TitleCrystal structure of RsbX in complex with magnesium in space group P1
ComponentsPhosphoserine phosphatase RsbX
KeywordsHYDROLASE / signaling protein / Stressosome / Environmental stress / Phosphoric Monoester Hydrolases / Dephosphorylation / Tertiary / phosphatase / Protein phosphatase / magnesium/manganese binding / alpha-beta beta-alpha sandwich fold
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
Phosphoserine phosphatase RsbX
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,3934
Polymers44,3442
Non-polymers492
Water10,809600
1
A: Phosphoserine phosphatase RsbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1962
Polymers22,1721
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoserine phosphatase RsbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1962
Polymers22,1721
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.081, 41.608, 69.038
Angle α, β, γ (deg.)81.000, 90.010, 71.140
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 22172.029 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): BL21(DE3) / References: UniProt: P17906, phosphoserine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 20% PEG 1000, 0.1M Tris-HCl, 5mM MgCl2, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 1, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 75857 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rsym value: 0.076
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.2 % / Rsym value: 0.325 / % possible all: 68.4

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3W45

3w45


Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2217 / WRfactor Rwork: 0.1719 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8467 / SU B: 2.289 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0806 / SU Rfree: 0.0739 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 3785 5 %RANDOM
Rwork0.1764 ---
obs0.1791 75821 89.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.41 Å2 / Biso mean: 15.0362 Å2 / Biso min: 2.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0.8 Å20.28 Å2
2--0.76 Å2-0.16 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 2 600 3710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223483
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9684752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07125.287157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49215681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7791515
X-RAY DIFFRACTIONr_chiral_restr0.1260.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022645
X-RAY DIFFRACTIONr_mcbond_it2.111.52159
X-RAY DIFFRACTIONr_mcangle_it3.12523531
X-RAY DIFFRACTIONr_scbond_it4.59631324
X-RAY DIFFRACTIONr_scangle_it6.6784.51181
X-RAY DIFFRACTIONr_rigid_bond_restr2.21833483
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 197 -
Rwork0.228 3830 -
all-4027 -
obs--64.89 %

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