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- PDB-8qob: Crystal structure of phosphoserine phosphatase (SerB) from Brucel... -

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Basic information

Entry
Database: PDB / ID: 8qob
TitleCrystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with AP3 and magnesium
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / Complex / Inhibitor / 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
: / Phosphoserine phosphatase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsScaillet, T. / Wouters, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: Crystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with AP3 and magnesium
Authors: Scaillet, T. / Wouters, J.
#3: Journal: J Synchrotron Radiat / Year: 2019
Title: MXCuBE2: the dawn of MXCuBE Collaboration.
Authors: Oscarsson, M. / Beteva, A. / Flot, D. / Gordon, E. / Guijarro, M. / Leonard, G. / McSweeney, S. / Monaco, S. / Mueller-Dieckmann, C. / Nanao, M. / Nurizzo, D. / Popov, A.N. / von Stetten, D. ...Authors: Oscarsson, M. / Beteva, A. / Flot, D. / Gordon, E. / Guijarro, M. / Leonard, G. / McSweeney, S. / Monaco, S. / Mueller-Dieckmann, C. / Nanao, M. / Nurizzo, D. / Popov, A.N. / von Stetten, D. / Svensson, O. / Rey-Bakaikoa, V. / Chado, I. / Chavas, L.M.G. / Gadea, L. / Gourhant, P. / Isabet, T. / Legrand, P. / Savko, M. / Sirigu, S. / Shepard, W. / Thompson, A. / Mueller, U. / Nan, J. / Eguiraun, M. / Bolmsten, F. / Nardella, A. / Milan-Otero, A. / Thunnissen, M. / Hellmig, M. / Kastner, A. / Schmuckermaier, L. / Gerlach, M. / Feiler, C. / Weiss, M.S. / Bowler, M.W. / Gobbo, A. / Papp, G. / Sinoir, J. / McCarthy, A.A. / Karpics, I. / Nikolova, M. / Bourenkov, G. / Schneider, T. / Andreu, J. / Cuni, G. / Juanhuix, J. / Boer, R. / Fogh, R. / Keller, P. / Flensburg, C. / Paciorek, W. / Vonrhein, C. / Bricogne, G. / de Sanctis, D.
#4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Features and development of Coot.
Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan /
Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
#5: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Integration, scaling, space-group assignment and post-refinement.
Authors: Kabsch, W.
History
DepositionSep 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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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)32,7784
Polymers32,5491
Non-polymers2293
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-22 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.267, 145.267, 145.267
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-460-

HOH

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Components

#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
#2: Chemical ChemComp-WHT / (2~{R})-2-azanyl-3-phosphono-propanoic acid


Mass: 169.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
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: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / 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 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.74→45.94 Å / Num. obs: 13539 / % possible obs: 99.86 % / Redundancy: 39.8 % / Biso Wilson estimate: 64.9 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1814 / Rpim(I) all: 0.02917 / Rrim(I) all: 0.1837 / Net I/σ(I): 19.41
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 39.7 % / Rmerge(I) obs: 1.504 / Mean I/σ(I) obs: 3.64 / Num. unique obs: 1314 / CC1/2: 0.891 / CC star: 0.971 / Rpim(I) all: 0.2408 / Rrim(I) all: 1.523 / % possible all: 99.03

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
XSCALEdata scaling
XDSdata reduction
Coot0.9.8.1model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→45.94 Å / SU ML: 0.3827 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.65
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 677 5.01 %
Rwork0.1802 12849 -
obs0.1829 13526 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.09 Å2
Refinement stepCycle: LAST / Resolution: 2.74→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 12 93 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892269
X-RAY DIFFRACTIONf_angle_d1.08423081
X-RAY DIFFRACTIONf_chiral_restr0.0573368
X-RAY DIFFRACTIONf_plane_restr0.0089406
X-RAY DIFFRACTIONf_dihedral_angle_d8.3918331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.950.37341330.26162521X-RAY DIFFRACTION99.51
2.95-3.250.34791340.22812554X-RAY DIFFRACTION100
3.25-3.720.27891360.21052564X-RAY DIFFRACTION100
3.72-4.680.23291340.16512567X-RAY DIFFRACTION99.93
4.69-45.940.18521400.15072643X-RAY DIFFRACTION100

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