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Basic information

Entry
Database: PDB / ID: 2j6y
TitleStructural and Functional Characterisation of partner switching regulating the environmental stress response in Bacillus subtilis
ComponentsPHOSPHOSERINE PHOSPHATASE RSBU
KeywordsHYDROLASE / PARTNER SWITCHING / PROTEIN PHOSPHATASE / RSBT / RSBU / STRESS / BACILLUS SUBTILIS
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / phosphatase activity / phosphoprotein phosphatase activity
Similarity search - Function
Phosphoserine phosphatase RsbU, N-terminal / Phosphoserine phosphatase RsbU, N-terminal domain / KaiA/RbsU domain / KaiA/RbsU helical domain superfamily / Stage II sporulation protein E (SpoIIE) / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily ...Phosphoserine phosphatase RsbU, N-terminal / Phosphoserine phosphatase RsbU, N-terminal domain / KaiA/RbsU domain / KaiA/RbsU helical domain superfamily / Stage II sporulation protein E (SpoIIE) / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Sigma factor PP2C-like phosphatases / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphoserine phosphatase RsbU
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHardwick, S.W. / Pane-Farre, J. / Delumeau, O. / Marles-Wright, J. / Murray, J.W. / Hecker, M. / Lewis, R.J.
CitationJournal: J. Biol. Chem. / Year: 2007
Title: Structural and functional characterization of partner switching regulating the environmental stress response in Bacillus subtilis.
Authors: Hardwick, S.W. / Pane-Farre, J. / Delumeau, O. / Marles-Wright, J. / Murray, J.W. / Hecker, M. / Lewis, R.J.
History
DepositionOct 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: PHOSPHOSERINE PHOSPHATASE RSBU
B: PHOSPHOSERINE PHOSPHATASE RSBU
C: PHOSPHOSERINE PHOSPHATASE RSBU
D: PHOSPHOSERINE PHOSPHATASE RSBU
E: PHOSPHOSERINE PHOSPHATASE RSBU


Theoretical massNumber of molelcules
Total (without water)65,8855
Polymers65,8855
Non-polymers00
Water6,269348
1
A: PHOSPHOSERINE PHOSPHATASE RSBU
B: PHOSPHOSERINE PHOSPHATASE RSBU


Theoretical massNumber of molelcules
Total (without water)26,3542
Polymers26,3542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: PHOSPHOSERINE PHOSPHATASE RSBU
D: PHOSPHOSERINE PHOSPHATASE RSBU


Theoretical massNumber of molelcules
Total (without water)26,3542
Polymers26,3542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: PHOSPHOSERINE PHOSPHATASE RSBU

E: PHOSPHOSERINE PHOSPHATASE RSBU


Theoretical massNumber of molelcules
Total (without water)26,3542
Polymers26,3542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)100.157, 47.831, 94.968
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.31579, -0.40596, 0.8576), (-0.453, -0.72968, -0.51221), (0.83371, -0.55024, 0.04653)11.16532, 96.41347, 39.91925
3given(0.66536, -0.55628, -0.49785), (0.66387, 0.13589, 0.7354), (-0.34144, -0.81981, 0.45971)16.80099, -11.33859, 36.69727
4given(-0.38636, 0.38977, 0.83595), (0.36767, -0.76612, 0.52715), (0.8459, 0.51102, 0.15269)-48.49957, 38.22107, -29.12519
5given(-0.74235, -0.60666, 0.28441), (-0.58029, 0.36995, -0.72554), (0.33494, -0.70364, -0.62667)16.79219, 55.1134, 90.17612

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Components

#1: Protein
PHOSPHOSERINE PHOSPHATASE RSBU / SIGMA FACTOR SIGB REGULATION PROTEIN RSBU / N-RSBU


Mass: 13177.083 Da / Num. of mol.: 5 / Fragment: RSBT BINDING DOMAIN, RESIDUES 1-111 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40399, phosphoserine phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 24 TO LYS ENGINEERED RESIDUE IN CHAIN B, GLU 24 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, GLU 24 TO LYS ENGINEERED RESIDUE IN CHAIN B, GLU 24 TO LYS ENGINEERED RESIDUE IN CHAIN C, GLU 24 TO LYS ENGINEERED RESIDUE IN CHAIN D, GLU 24 TO LYS ENGINEERED RESIDUE IN CHAIN E, GLU 24 TO LYS
Sequence detailsRESIDUE E24 HAS BEEN MUTATED TO K

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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: 1.75 Å3/Da / Density % sol: 29.72 %
Crystal growpH: 6.5 / Details: 10 % PEG 20000, 100 MM MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→48.11 Å / Num. obs: 35972 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
ARP/wARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W53

1w53


Resolution: 1.85→42.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.286 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1788 5 %RANDOM
Rwork0.183 ---
obs0.186 34179 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 0 348 3866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223577
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.974844
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.13623.526173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53415656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9291522
X-RAY DIFFRACTIONr_chiral_restr0.1240.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022677
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21945
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22568
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3531.52174
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05723446
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3731582
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9424.51391
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 125 -
Rwork0.249 2429 -
obs--93.18 %

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