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- PDB-7qpl: Crystal structure of phosphoserine phosphatase (SerB) from Brucel... -

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Basic information

Entry
Database: PDB / ID: 7qpl
TitleCrystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with phosphate and magnesium
ComponentsO-phosphoserine phosphohydrolase
KeywordsHYDROLASE / HAD phosphatase / ACT-like domain / Rossmanoid fold / L-serine biosynthesis
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / metal ion binding
Similarity search - Function
Phosphoserine phosphatase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Phosphoserine phosphatase
Similarity search - Component
Biological speciesBrucella melitensis bv. 1 str. 16M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsPierson, E. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Other government Belgium
CitationJournal: To Be Published
Title: Crystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with phosphate and magnesium
Authors: Pierson, E. / Wouters, J.
History
DepositionJan 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-phosphoserine phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,68217
Polymers32,5491
Non-polymers1,13216
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.210, 143.210, 143.210
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-777-

HOH

21A-778-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein O-phosphoserine phosphohydrolase / Phosphoserine phosphatase


Mass: 32549.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SerB sequence is preceded by the rest of HRV-3C protease cleavage site (GPGS) at N-term
Source: (gene. exp.) Brucella melitensis bv. 1 str. 16M (bacteria)
Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI0615 / Plasmid: AVA0421
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8YI30, phosphoserine phosphatase

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Non-polymers , 7 types, 296 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 6.8
Details: 0.2M Sodium Formate, 0.1M Sodium phosphate pH 6.8, 22% w/v BCS PEG smear MMW, 10% v/v glycerol
PH range: 6.6-7.0 / 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: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.77→38.27 Å / Num. obs: 47522 / % possible obs: 95.42 % / Redundancy: 41.4 % / Biso Wilson estimate: 39.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09586 / Rpim(I) all: 0.01509 / Rrim(I) all: 0.09705 / Net I/σ(I): 22.77
Reflection shellResolution: 1.77→1.833 Å / Redundancy: 41.3 % / Rmerge(I) obs: 2.942 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 2558 / CC1/2: 0.616 / Rpim(I) all: 0.4624 / Rrim(I) all: 2.978 / % possible all: 54.56

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.19.2_4158refinement
MxCuBEdata collection
autoPROC1.0.5(20210716)data processing
PHASERphasing
Coot0.9.4.1model building
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold model

Resolution: 1.77→38.27 Å / SU ML: 0.1984 / Cross valid method: FREE R-VALUE / Phase error: 21.7719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1833 --
Rwork0.1578 43157 -
obs-45353 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 1.77→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 72 280 2545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912308
X-RAY DIFFRACTIONf_angle_d1.13763109
X-RAY DIFFRACTIONf_chiral_restr0.0662369
X-RAY DIFFRACTIONf_plane_restr0.0092401
X-RAY DIFFRACTIONf_dihedral_angle_d8.5136346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.3945300.3061053X-RAY DIFFRACTION36.21
1.8-1.850.31491330.28112262X-RAY DIFFRACTION80.72
1.85-1.890.27571570.24172809X-RAY DIFFRACTION99.97
1.89-1.940.2381410.21412832X-RAY DIFFRACTION100
1.94-20.2091640.19752810X-RAY DIFFRACTION100
2-2.060.20321560.18622834X-RAY DIFFRACTION100
2.06-2.140.23951480.18482842X-RAY DIFFRACTION100
2.14-2.220.20611670.18182776X-RAY DIFFRACTION100
2.22-2.330.1871320.16122872X-RAY DIFFRACTION100
2.33-2.450.18521830.17982784X-RAY DIFFRACTION100
2.45-2.60.20481310.17662866X-RAY DIFFRACTION100
2.6-2.80.20641600.18612825X-RAY DIFFRACTION100
2.8-3.080.19181420.1692862X-RAY DIFFRACTION100
3.08-3.530.17831540.15652853X-RAY DIFFRACTION100
3.53-4.450.15961310.13372916X-RAY DIFFRACTION100
4.45-38.270.16121590.13632961X-RAY DIFFRACTION99.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.85842077399-1.712777266111.40528650267.66066851639-2.062582070623.212878939640.1130235523140.1265556005720.00087712625120.355121013475-0.150361196875-1.109022699280.4716037315320.4265916157290.03211469999750.6181580967950.0465604571741-0.03363565151320.268649370971-0.02082463318950.4650482645359.33640372768-24.58606350530.1167085112
21.19945495993-0.4271641100721.577134246332.19813829549-0.5888043679724.58253603458-0.132080269134-0.0962656521528-0.03402731221690.2744952213480.2017975251260.273860980292-0.317578769734-0.547158852068-0.0693760646120.3639579165780.006313508954960.08299504443740.2914431334030.0309998070240.370869149198-11.7763959662-5.955840900215.4590813871
31.923057627430.161971505786-0.3983252643164.28153020555-0.6905202180594.09911470844-0.09802260797850.00440475831404-0.1128130923860.4978925498180.0843997999815-0.2030407460180.1671870529480.07622705049880.0045063414260.461351010469-0.0165051142145-0.01081329542830.1945591792-0.02245866233440.3446009912152.5242283621-14.363741712224.02821386
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 86 )1 - 861 - 86
22chain 'A' and (resid 87 through 230 )87 - 23087 - 230
33chain 'A' and (resid 231 through 295 )231 - 295231 - 295

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