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

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Basic information

Entry
Database: PDB / ID: 9fqn
TitleCrystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with L-Ser and Magnesium
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / Complex / Serine biosynthesis / Magnesium cofactor / L-Serine / Product
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 / SERINE / Phosphoserine phosphatase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsScaillet, T. / Wouters, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with L-Ser and Magnesium
Authors: Scaillet, T. / Wouters, J.
History
DepositionJun 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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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)33,0548
Polymers32,5491
Non-polymers5057
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-26 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.830, 142.830, 142.830
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-573-

HOH

21A-575-

HOH

31A-600-

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, 209 molecules

#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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 / pH: 8
Details: 0.2M sodium malonate, 0.1M Bis-tris propane, PEG3350
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 2 / Wavelength: 1.0439 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0439 Å / Relative weight: 1
ReflectionResolution: 2.11→45.17 Å / Num. obs: 27894 / % possible obs: 99.84 % / Redundancy: 40.1 % / Biso Wilson estimate: 48.65 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.08128 / Rpim(I) all: 0.01306 / Rrim(I) all: 0.08233 / Net I/σ(I): 35.36
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 38.3 % / Rmerge(I) obs: 1.374 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 2749 / CC1/2: 0.856 / CC star: 0.96 / Rpim(I) all: 0.2232 / Rrim(I) all: 1.393 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→45.17 Å / SU ML: 0.3229 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.8999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 1394 5 %
Rwork0.1961 26495 -
obs0.1987 27889 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.17 Å2
Refinement stepCycle: LAST / Resolution: 2.11→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 30 202 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752281
X-RAY DIFFRACTIONf_angle_d0.85353089
X-RAY DIFFRACTIONf_chiral_restr0.0518370
X-RAY DIFFRACTIONf_plane_restr0.0072404
X-RAY DIFFRACTIONf_dihedral_angle_d6.8219338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.190.40441370.35782611X-RAY DIFFRACTION98.6
2.19-2.270.28431390.28662632X-RAY DIFFRACTION99.96
2.28-2.380.29031380.24612614X-RAY DIFFRACTION99.96
2.38-2.50.29941390.24562645X-RAY DIFFRACTION100
2.5-2.660.34991390.26882645X-RAY DIFFRACTION100
2.66-2.870.27761380.25982618X-RAY DIFFRACTION100
2.87-3.150.27231390.22382648X-RAY DIFFRACTION100
3.15-3.610.26691400.20452660X-RAY DIFFRACTION100
3.61-4.540.19571400.15272655X-RAY DIFFRACTION100
4.55-45.170.2131450.15232767X-RAY DIFFRACTION99.93

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