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- PDB-8a1z: Crystal structure of Phosphoserine phosphatase SerB from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 8a1z
TitleCrystal structure of Phosphoserine phosphatase SerB from Mycobacterium avium in complex with 1-(2,4-dichlorophenyl)-3-hydroxyurea
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / phosphoserine phosphatase / fragment / avium
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / metal ion binding
Similarity search - Function
Phosphoserine phosphatase / ACT domain profile. / ACT domain / ACT-like domain / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
1-(2,4-dichlorophenyl)-3-oxidanyl-urea / Phosphoserine phosphatase
Similarity search - Component
Biological speciesMycobacterium avium 104 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsHaufroid, M. / Wouters, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Targeting the phosphoserine phosphatase MtSerB2 for tuberculosis drug discovery, an hybrid knowledge based /fragment based approach.
Authors: Haufroid, M. / Volkov, A.N. / Wouters, J.
History
DepositionJun 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 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

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Assembly

Deposited unit
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1334
Polymers43,8521
Non-polymers2813
Water2,378132
1
A: Phosphoserine phosphatase
hetero molecules

A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2668
Polymers87,7042
Non-polymers5626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6380 Å2
ΔGint-63 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.600, 107.700, 132.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-691-

HOH

21A-714-

HOH

31A-730-

HOH

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Components

#1: Protein Phosphoserine phosphatase / O-phosphoserine phosphohydrolase


Mass: 43852.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium 104 (bacteria) / Gene: O972_03940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V7LE91, phosphoserine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-KVU / 1-(2,4-dichlorophenyl)-3-oxidanyl-urea


Mass: 221.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6Cl2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 132 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.1 M MES monohydrate pH 6.1, 16% PEG 6000, 0.2 M magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.28→43.59 Å / Num. obs: 22525 / % possible obs: 98.82 % / Redundancy: 13.1 % / Biso Wilson estimate: 48.04 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1156 / Rpim(I) all: 0.0332 / Rrim(I) all: 0.1203 / Net I/σ(I): 13
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.718 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 1985 / CC1/2: 0.656 / CC star: 0.89 / Rpim(I) all: 0.5093 / % possible all: 88.62

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3p96

3p96


Resolution: 2.28→43.59 Å / SU ML: 0.3588 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6763
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 1126 5 %
Rwork0.2055 21395 -
obs0.2076 22521 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.52 Å2
Refinement stepCycle: LAST / Resolution: 2.28→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 15 132 3036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772937
X-RAY DIFFRACTIONf_angle_d0.95094005
X-RAY DIFFRACTIONf_chiral_restr0.0564502
X-RAY DIFFRACTIONf_plane_restr0.0117524
X-RAY DIFFRACTIONf_dihedral_angle_d6.4262429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.380.39031270.36622401X-RAY DIFFRACTION90.87
2.38-2.510.34271400.28152675X-RAY DIFFRACTION100
2.51-2.670.29261410.25812673X-RAY DIFFRACTION100
2.67-2.870.32471410.25662686X-RAY DIFFRACTION100
2.87-3.160.31921420.2322689X-RAY DIFFRACTION100
3.16-3.620.25891420.20052702X-RAY DIFFRACTION99.93
3.62-4.560.2141440.16622732X-RAY DIFFRACTION100
4.56-43.590.18991490.17822837X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: 28.7103375344 Å / Origin y: 43.1773359021 Å / Origin z: 27.6445515325 Å
111213212223313233
T0.342151462651 Å2-0.162752952719 Å20.0511720192754 Å2-0.395664752411 Å2-0.029591542087 Å2--0.479105553437 Å2
L0.937875715705 °20.911427459122 °21.16932651766 °2-2.21255491076 °21.43443975812 °2--3.25966937128 °2
S0.0389046830653 Å °-0.0019434757516 Å °-0.128032194745 Å °-0.0646772387468 Å °-0.00284644634577 Å °-0.0783203936167 Å °0.187765270502 Å °0.0226228020251 Å °-0.0383255277314 Å °
Refinement TLS groupSelection details: all

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