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

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Basic information

Entry
Database: PDB / ID: 9fqc
TitleCrystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in copmplex with O-Phosphoserine
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / Complex / Serine biosynthesis / Magnesium cofactor / Substrate / O-Phosphoserine / OPS
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
PHOSPHOSERINE / Phosphoserine phosphatase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 15, 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

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Assembly

Deposited unit
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9386
Polymers32,5491
Non-polymers3885
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-37 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.250, 145.250, 145.250
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-542-

HOH

21A-561-

HOH

31A-567-

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 , 5 types, 175 molecules

#2: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 170 / 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, hanging drop / 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: 2.35→36.31 Å / Num. obs: 21468 / % possible obs: 99.94 % / Redundancy: 40.5 % / Biso Wilson estimate: 51.7 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1336 / Rpim(I) all: 0.02137 / Rrim(I) all: 0.1353 / Net I/σ(I): 25.29
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 40.1 % / Rmerge(I) obs: 1.516 / Mean I/σ(I) obs: 2.55 / Num. unique obs: 2136 / CC1/2: 0.834 / CC star: 0.954 / Rpim(I) all: 0.2409 / Rrim(I) all: 1.536 / % possible all: 100

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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: 2.35→36.31 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.5726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1929 1073 5 %
Rwork0.1597 20395 -
obs0.1613 21468 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.66 Å2
Refinement stepCycle: LAST / Resolution: 2.35→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 20 170 2383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072243
X-RAY DIFFRACTIONf_angle_d0.8233040
X-RAY DIFFRACTIONf_chiral_restr0.0521365
X-RAY DIFFRACTIONf_plane_restr0.0074397
X-RAY DIFFRACTIONf_dihedral_angle_d6.1229323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.450.25611320.21872504X-RAY DIFFRACTION98.69
2.45-2.580.22611330.20562538X-RAY DIFFRACTION100
2.58-2.740.21851330.21412531X-RAY DIFFRACTION100
2.74-2.950.25471320.20042511X-RAY DIFFRACTION100
2.96-3.250.22271340.18492545X-RAY DIFFRACTION100
3.25-3.720.20781350.16642562X-RAY DIFFRACTION100
3.72-4.680.16991350.13092568X-RAY DIFFRACTION100
4.69-36.310.15681390.13572636X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -2.51907770495 Å / Origin y: -12.9596974841 Å / Origin z: 21.7642136431 Å
111213212223313233
T0.462277012229 Å2-0.0338866916996 Å20.0499696910308 Å2-0.255804187938 Å2-0.0079417395903 Å2--0.408597233418 Å2
L1.17387505824 °2-0.498468538115 °20.476925496282 °2-2.19516235445 °2-0.686024053036 °2--2.55738822286 °2
S2.67126626255E-5 Å °0.0130559517965 Å °0.0129686259074 Å °0.335307662933 Å °0.0320775389588 Å °-0.157504568054 Å °0.0430095718911 Å °0.0278173964192 Å °-0.0338020503296 Å °
Refinement TLS groupSelection details: all

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