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- PDB-3w42: Crystal structure of RsbX in complex with manganese in space group P1 -

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Basic information

Entry
Database: PDB / ID: 3w42
TitleCrystal structure of RsbX in complex with manganese 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: 1.06 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)44,4544
Polymers44,3442
Non-polymers1102
Water10,971609
1
A: Phosphoserine phosphatase RsbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2272
Polymers22,1721
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoserine phosphatase RsbX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2272
Polymers22,1721
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.198, 41.649, 68.755
Angle α, β, γ (deg.)81.17, 89.96, 71.46
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 20 % PEG 1000, 0.1M Tris-HCl, 5mM MgCl2, 3mM 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: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2009 / Details: KIRKPATRICK-BAEZ MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.06→50 Å / Num. obs: 155995 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.081 / Net I/σ(I): 23.6
Reflection shellResolution: 1.06→1.1 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.366 / % possible all: 71.5

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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: 1.06→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.02 / SU B: 0.756 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0284 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15492 7240 5 %RANDOM
Rwork0.12707 ---
obs0.12847 136539 92.18 %-
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: 8.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0.26 Å20 Å2
2--0.38 Å2-0.01 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.06→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 2 609 3719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223553
X-RAY DIFFRACTIONr_bond_other_d0.0010.022487
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.9684848
X-RAY DIFFRACTIONr_angle_other_deg1.30636180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1415505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55825.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78315710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9741516
X-RAY DIFFRACTIONr_chiral_restr0.1610.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024044
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02684
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_it2.2661.52187
X-RAY DIFFRACTIONr_mcbond_other0.7591.5892
X-RAY DIFFRACTIONr_mcangle_it3.3223580
X-RAY DIFFRACTIONr_scbond_it4.87431366
X-RAY DIFFRACTIONr_scangle_it7.0894.51219
X-RAY DIFFRACTIONr_rigid_bond_restr2.05336040
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.061→1.088 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 427 -
Rwork0.215 8666 -
obs--79.81 %

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