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- PDB-6m1x: Crystal structure of Phosphoserine Phosphatase in complex with 3-... -

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Basic information

Entry
Database: PDB / ID: 6m1x
TitleCrystal structure of Phosphoserine Phosphatase in complex with 3-Phosphoglyceric Acid from Entamoeba histolytica
ComponentsPhosphoglycerate mutase family protein
KeywordsCYTOSOLIC PROTEIN / Phosphoserine Phosphatase / 3-Phosphoglyceric Acid / complex
Function / homology
Function and homology information


phosphatase activity / cytoplasm
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
3-PHOSPHOGLYCERIC ACID / PHOSPHATE ION / Phosphoglycerate mutase family protein
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsKumari, P. / Gourinath, S.
Funding support1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)
Citation
Journal: Int.J.Biol.Macromol. / Year: 2021
Title: Structural analysis of EhPSP in complex with 3-phosphoglyceric acid from Entamoeba histolytica reveals a basis for its lack of phosphoglycerate mutase activity.
Authors: Kumari, P. / Vijayan, R. / Gourinath, S.
#1: Journal: 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
DepositionFeb 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: 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: Phosphoglycerate mutase family protein
B: Phosphoglycerate mutase family protein
C: Phosphoglycerate mutase family protein
D: Phosphoglycerate mutase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6468
Polymers95,0844
Non-polymers5624
Water64936
1
A: Phosphoglycerate mutase family protein
B: Phosphoglycerate mutase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7324
Polymers47,5422
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-24 kcal/mol
Surface area16260 Å2
MethodPISA
2
C: Phosphoglycerate mutase family protein
hetero molecules

D: Phosphoglycerate mutase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9144
Polymers47,5422
Non-polymers3722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2490 Å2
ΔGint-19 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.976, 112.388, 177.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Phosphoglycerate mutase family protein


Mass: 23771.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 3-Phosphoglyceric Acid / Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_129820 / Plasmid: pET28B / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C4M5P9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MMT buffer pH-4.0, PEG-1500 (20%), 0.2 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 82 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.48→88.87 Å / Num. obs: 33163 / % possible obs: 96.1 % / Redundancy: 4.1 % / CC1/2: 1 / Net I/σ(I): 10.83
Reflection shellResolution: 2.48→2.59 Å / Rmerge(I) obs: 0.506 / Num. unique obs: 3206 / CC1/2: 0.843

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZKK

5zkk


Resolution: 2.48→88.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.453 / SU ML: 0.254 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.526 / ESU R Free: 0.287
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 1718 5.2 %RANDOM
Rwork0.2284 ---
obs0.2299 31433 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.35 Å2 / Biso mean: 54.274 Å2 / Biso min: 25.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å2-0 Å2
2---4.44 Å2-0 Å2
3---6.42 Å2
Refinement stepCycle: final / Resolution: 2.48→88.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5895 0 32 36 5963
Biso mean--70.82 47.29 -
Num. residues----782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196079
X-RAY DIFFRACTIONr_bond_other_d0.0060.025634
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9458262
X-RAY DIFFRACTIONr_angle_other_deg1.027312940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57125.484248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85815981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.906159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026937
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021380
LS refinement shellResolution: 2.48→2.541 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.398 110 -
Rwork0.409 1946 -
obs--81.43 %

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