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- PDB-5zkk: Crystal structure of Phosphoserine phosphatase from Entamoeba his... -

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Basic information

Entry
Database: PDB / ID: 5zkk
TitleCrystal structure of Phosphoserine phosphatase from Entamoeba histolytica
ComponentsPhosphoglycerate mutase family protein, putative
KeywordsHYDROLASE / Histidine phosphatase superfamily memeber / Phosphatase / cysteine biosynthetic pathway / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


phosphatase activity / cytosol
Similarity search - Function
: / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Phosphoglycerate mutase family protein, putative
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS-A (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKumari, P. / Gourinath, S.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural and functional characterisation of phosphoserine phosphatase, that plays critical role in the oxidative stress response in the parasite Entamoeba histolytica.
Authors: Kumari, P. / Babuta, M. / Bhattacharya, A. / Gourinath, S.
History
DepositionMar 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate mutase family protein, putative
B: Phosphoglycerate mutase family protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,11416
Polymers47,5422
Non-polymers1,57214
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-15 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.172, 109.172, 165.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphoglycerate mutase family protein, putative / Phosphoserine phosphatase


Mass: 23771.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS-A (eukaryote)
Gene: EHI7A_041450 / Plasmid: pET 28b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: N9V397

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Non-polymers , 7 types, 229 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 0.1 M phosphate citrate buffer, pH 4.2, 4% PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→94.55 Å / Num. obs: 39785 / % possible obs: 98.7 % / Redundancy: 14.6 % / CC1/2: 0.996 / Χ2: 1.305 / Net I/σ(I): 27.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2002 / CC1/2: 0.802 / Χ2: 0.856 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IJ5

4ij5


Resolution: 2→94.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20193 1948 4.9 %RANDOM
Rwork0.16657 ---
obs0.16823 37779 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.26 Å2-0 Å2
2---0.52 Å2-0 Å2
3---1.69 Å2
Refinement stepCycle: 1 / Resolution: 2→94.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 99 215 3363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193203
X-RAY DIFFRACTIONr_bond_other_d00.023072
X-RAY DIFFRACTIONr_angle_refined_deg2.1661.9624305
X-RAY DIFFRACTIONr_angle_other_deg3.68537082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91225.672134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12915543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.327155
X-RAY DIFFRACTIONr_chiral_restr0.1380.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023539
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02710
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8642.8661573
X-RAY DIFFRACTIONr_mcbond_other2.8622.8631572
X-RAY DIFFRACTIONr_mcangle_it3.9124.2731963
X-RAY DIFFRACTIONr_mcangle_other3.9124.2761964
X-RAY DIFFRACTIONr_scbond_it4.8733.4111630
X-RAY DIFFRACTIONr_scbond_other4.8733.4111630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0364.8712343
X-RAY DIFFRACTIONr_long_range_B_refined8.2824.0623701
X-RAY DIFFRACTIONr_long_range_B_other8.28324.0683702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 147 -
Rwork0.22 2782 -
obs--99.9 %

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