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- PDB-9fq5: Crystal structure of phosphoserine phosphatase (SerB) from Brucel... -

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Basic information

Entry
Database: PDB / ID: 9fq5
TitleCrystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / Complex / Serine biosynthesis / Magnesium cofactor
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
haloacid dehalogenase-like hydrolase / Phosphoserine phosphatase / : / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phosphoserine phosphatase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsScaillet, T. / Wouters, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proteins / Year: 2025
Title: Structural and Enzymological Characterization of Phosphoserine Phosphatase From Brucella melitensis.
Authors: Scaillet, T. / Pierson, E. / Fillet, M. / Wouters, J.
History
DepositionJun 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0599
Polymers32,5491
Non-polymers5108
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-19 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.100, 143.100, 143.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11A-584-

HOH

21A-609-

HOH

31A-655-

HOH

41A-658-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoserine phosphatase / O-phosphoserine phosphohydrolase


Mass: 32549.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: BMEI0615 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YI30, phosphoserine phosphatase

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Non-polymers , 6 types, 269 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3350, sodium malonate, Bis-Tris propane / PH range: 6.5-8.0 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→45.25 Å / Num. obs: 38642 / % possible obs: 99.97 % / Redundancy: 41.7 % / Biso Wilson estimate: 40.84 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07031 / Rpim(I) all: 0.01101 / Rrim(I) all: 0.07117 / Net I/σ(I): 36.54
Reflection shellResolution: 1.9→1.967 Å / Redundancy: 42.4 % / Rmerge(I) obs: 1.388 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 3834 / CC1/2: 0.862 / CC star: 0.962 / Rpim(I) all: 0.2151 / Rrim(I) all: 1.405 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
XSCALEdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.25 Å / SU ML: 0.2364 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2241 1933 5 %
Rwork0.1873 36709 -
obs0.1891 38642 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 30 261 2556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742336
X-RAY DIFFRACTIONf_angle_d0.91753156
X-RAY DIFFRACTIONf_chiral_restr0.0577377
X-RAY DIFFRACTIONf_plane_restr0.0074411
X-RAY DIFFRACTIONf_dihedral_angle_d6.7524344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.32631350.32572569X-RAY DIFFRACTION98.58
1.94-20.28911380.28252615X-RAY DIFFRACTION100
2-2.050.27081360.25722575X-RAY DIFFRACTION100
2.05-2.120.2671380.25862625X-RAY DIFFRACTION100
2.12-2.20.29111370.26342603X-RAY DIFFRACTION100
2.2-2.280.25591370.23892617X-RAY DIFFRACTION100
2.28-2.390.27281380.23562616X-RAY DIFFRACTION100
2.39-2.510.27551370.22912594X-RAY DIFFRACTION100
2.51-2.670.25641370.2362614X-RAY DIFFRACTION100
2.67-2.880.23541390.22222630X-RAY DIFFRACTION100
2.88-3.170.24471380.19772630X-RAY DIFFRACTION100
3.17-3.630.21791390.17892629X-RAY DIFFRACTION100
3.63-4.570.19061400.13642662X-RAY DIFFRACTION100
4.57-45.250.17881440.14722730X-RAY DIFFRACTION99.83

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