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- PDB-6hyy: Human phosphoserine phosphatase with serine and phosphate -

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Basic information

Entry
Database: PDB / ID: 6hyy
TitleHuman phosphoserine phosphatase with serine and phosphate
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / Human phosphoserine phosphatase
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
PHOSPHATE ION / SERINE / Phosphoserine phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.566 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 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)49,5267
Polymers49,1662
Non-polymers3595
Water6,251347
1
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8074
Polymers24,5831
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7183
Polymers24,5831
Non-polymers1352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.140, 129.140, 155.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-555-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphoserine phosphatase / / PSPase / L-3-phosphoserine phosphatase / O-phosphoserine phosphohydrolase


Mass: 24583.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSPH / Plasmid: PET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78330, phosphoserine phosphatase

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Non-polymers , 5 types, 352 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05 M CaCl2; 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: 1.566→38.947 Å / Num. obs: 69622 / % possible obs: 99.25 % / Redundancy: 2 % / Biso Wilson estimate: 25.93 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01387 / Rpim(I) all: 0.01387 / Rrim(I) all: 0.01962 / Net I/σ(I): 22.3
Reflection shellResolution: 1.566→1.622 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2437 / Num. unique obs: 6498 / CC1/2: 0.897 / Rpim(I) all: 0.2437 / Rrim(I) all: 0.3447 / % possible all: 93.82

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Processing

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

1nnl


Resolution: 1.566→38.947 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.2
RfactorNum. reflection% reflection
Rfree0.2256 3481 5 %
Rwork0.1946 --
obs0.1961 69605 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.19 Å2 / Biso mean: 35.0199 Å2 / Biso min: 15.66 Å2
Refinement stepCycle: final / Resolution: 1.566→38.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 19 347 3787
Biso mean--35.64 41.43 -
Num. residues----438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5661-1.58760.41171190.39222252237185
1.5876-1.61020.33061390.312226282767100
1.6102-1.63430.27321400.262926562796100
1.6343-1.65980.26831360.249825942730100
1.6598-1.6870.26681410.233926682809100
1.687-1.71610.2661370.225126032740100
1.7161-1.74730.2571390.211626452784100
1.7473-1.78090.24081380.211926282766100
1.7809-1.81730.22821410.208726712812100
1.8173-1.85680.2361370.214126092746100
1.8568-1.90.25761400.211326492789100
1.9-1.94750.2411390.199326422781100
1.9475-2.00020.20881390.198726372776100
2.0002-2.0590.22441390.201826522791100
2.059-2.12550.24071400.193926572797100
2.1255-2.20140.21761390.195126372776100
2.2014-2.28960.22991390.199526562795100
2.2896-2.39370.2361420.201226822824100
2.3937-2.51990.23891390.194726542793100
2.5199-2.67780.21031410.19426742815100
2.6778-2.88450.24091420.206526912833100
2.8845-3.17460.21171400.19726672807100
3.1746-3.63370.20161430.178827182861100
3.6337-4.57690.20211430.163927072850100
4.5769-38.95950.23491490.1922847299699

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