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- PDB-1l8o: Molecular basis for the local conformational rearrangement of hum... -

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Basic information

Entry
Database: PDB / ID: 1l8o
TitleMolecular basis for the local conformational rearrangement of human phosphoserine phosphatase
ComponentsL-3-phosphoserine phosphatase
KeywordsHYDROLASE / phosphatase / conformational rearrangement
Function / homology
Function and homology information


Serine biosynthesis / phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / response to nutrient levels / in utero embryonic development / magnesium ion binding ...Serine biosynthesis / phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / 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 / : / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle ...Phosphoserine phosphatase; domain 2 / Phosphoserine phosphatase / : / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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: 2.8 Å
AuthorsKim, H.Y. / Heo, Y.S. / Kim, J.H. / Park, M.H. / Moon, J. / Park, S.Y. / Lee, T.G. / Jeon, Y.H. / Ro, S. / Hwang, K.Y.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase
Authors: Kim, H.Y. / Heo, Y.S. / Kim, J.H. / Park, M.H. / Moon, J. / Kim, E. / Kwon, D. / Yoon, J. / Shin, D. / Jeong, E.J. / Park, S.Y. / Lee, T.G. / Jeon, Y.H. / Ro, S. / Cho, J.M. / Hwang, K.Y.
History
DepositionMar 21, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-3-phosphoserine phosphatase
B: L-3-phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5746
Polymers50,1732
Non-polymers4004
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.213, 106.213, 87.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

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


Mass: 25086.713 Da / Num. of mol.: 2 / Mutation: L164F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P78330, phosphoserine phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3

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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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
22.2-2.4 Msodium potassium phosphate1reservoirpH5.0
30.1 M1reservoirLiCl
42 %PEG4001reservoir
510 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.1 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 20, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 53399 / Num. obs: 52545 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 35.4 Å2
Reflection shellResolution: 2.8→2.98 Å / % possible all: 87.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 11843 / Num. measured all: 52545 / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.34 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 834055.67 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 808 7 %RANDOM
Rwork0.204 ---
all0.219 12018 --
obs0.204 11754 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.5317 Å2 / ksol: 0.265167 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å2--
2--2.26 Å2-
3----4.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a1.01 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 24 0 3508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.563
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 182 7 %
Rwork0.204 1558 -
obs-52545 87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PO4.PARAMPO4.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 500 Å / Num. reflection obs: 10343 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

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