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- PDB-6hyj: PSPH Human phosphoserine phosphatase -

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Basic information

Entry
Database: PDB / ID: 6hyj
TitlePSPH Human phosphoserine phosphatase
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / phosphoserine phosphatase / homo sapiens
Function / homology
Function and homology information


phosphoserine phosphatase / Serine biosynthesis / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / dephosphorylation / response to nutrient levels / in utero embryonic development ...phosphoserine phosphatase / Serine biosynthesis / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / dephosphorylation / response to nutrient levels / in utero embryonic development / magnesium ion binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Phosphoserine phosphatase; domain 2 / Phosphoserine phosphatase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Phosphoserine phosphatase; domain 2 / Phosphoserine phosphatase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOSERINE / SERINE / Phosphoserine phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.929 Å
AuthorsWouters, J. / Haufroid, M. / Mirgaux, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures and snapshots along the reaction pathway of human phosphoserine phosphatase.
Authors: Haufroid, M. / Mirgaux, M. / Leherte, L. / Wouters, J.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq
Item: _atom_site.label_entity_id / _cell.Z_PDB ..._atom_site.label_entity_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Revision 2.1Dec 7, 2022Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value
Revision 2.2Jan 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
B: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4037
Polymers49,8472
Non-polymers5555
Water3,333185
1
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1493
Polymers24,9241
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2544
Polymers24,9241
Non-polymers3303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.670, 128.970, 155.710
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 Phosphoserine phosphatase / / PSPase / L-3-phosphoserine phosphatase / O-phosphoserine phosphohydrolase


Mass: 24923.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSPH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78330, phosphoserine phosphatase
#2: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE / Phosphoserine


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8NO6P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CaCl2 0.15 M; sodium cacodylate 0.1 M pH 6.5; PEG 2000 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.929→34.23 Å / Num. obs: 36957 / % possible obs: 98.66 % / Redundancy: 2 % / Biso Wilson estimate: 43.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02987 / Rpim(I) all: 0.02987 / Rrim(I) all: 0.04224 / Net I/σ(I): 11.27
Reflection shellResolution: 1.929→1.998 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5529 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 3228 / CC1/2: 0.589 / Rpim(I) all: 0.5529 / Rrim(I) all: 0.7819 / % possible all: 87.57

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NNL

1nnl


Resolution: 1.929→34.23 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8
RfactorNum. reflection% reflection
Rfree0.2634 1847 5 %
Rwork0.1998 --
obs0.203 36943 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.65 Å2 / Biso mean: 48.8391 Å2 / Biso min: 23.74 Å2
Refinement stepCycle: final / Resolution: 1.929→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 37 185 3676
Biso mean--57.77 48.83 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9292-1.98140.49851200.48622291241184
1.9814-2.03970.40281420.341926902832100
2.0397-2.10550.30381410.279326782819100
2.1055-2.18070.30251410.246426862827100
2.1807-2.2680.27921440.216627322876100
2.268-2.37120.24741420.219226872829100
2.3712-2.49620.27311430.218627172860100
2.4962-2.65260.28741430.204927302873100
2.6526-2.85730.29491440.230427272871100
2.8573-3.14460.29971440.217727392883100
3.1446-3.59920.23041450.190127472892100
3.5992-4.5330.24681460.164927692915100
4.533-34.2350.23641520.173429033055100

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