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- PDB-4ij6: Crystal Structure of a Novel-type Phosphoserine Phosphatase Mutan... -

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Basic information

Entry
Database: PDB / ID: 4ij6
TitleCrystal Structure of a Novel-type Phosphoserine Phosphatase Mutant (H9A) from Hydrogenobacter thermophilus TK-6 in Complex with L-phosphoserine
ComponentsPhosphoserine phosphatase 1
KeywordsHYDROLASE / phosphatase
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / cytoplasm
Similarity search - Function
: / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOSERINE / Phosphoserine phosphatase 1
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChiba, Y. / Horita, S. / Ohtsuka, J. / Arai, H. / Nagata, K. / Igarashi, Y. / Tanokura, M. / Ishii, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis
Authors: Chiba, Y. / Horita, S. / Ohtsuka, J. / Arai, H. / Nagata, K. / Igarashi, Y. / Tanokura, M. / Ishii, M.
History
DepositionDec 21, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoserine phosphatase 1
B: Phosphoserine phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,92813
Polymers49,0532
Non-polymers87611
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-7 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.330, 68.920, 123.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoserine phosphatase 1 / PSP 1 / PSPase 1 / Metal-independent phosphoserine phosphatase 1 / iPSP1 / O-phosphoserine phosphohydrolase 1


Mass: 24526.275 Da / Num. of mol.: 2 / Mutation: H9A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria)
Strain: DSM 6534 / IAM 12695 / TK-6 / Gene: pspA, pgmA, HTH_0103, Hydth_0104 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DFG8, phosphoserine phosphatase
#2: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM sodium acetate trihydrate, 20 mM calcium chloride dihydrate, and 30% (v/v)-2-methyl-2,4-pentanediol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→38.2 Å / Num. all: 39857 / Num. obs: 39566

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IJ5

4ij5


Resolution: 1.8→38.15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.726 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1989 5 %RANDOM
Rwork0.1904 ---
obs0.1918 39565 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.03 Å2 / Biso mean: 17.555 Å2 / Biso min: 6.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å2-0 Å2
2--0.43 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 52 147 3546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193484
X-RAY DIFFRACTIONr_bond_other_d0.0010.023389
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9654700
X-RAY DIFFRACTIONr_angle_other_deg0.6823.0017788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67423.554166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4215641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4241528
X-RAY DIFFRACTIONr_chiral_restr0.0610.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02797
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 141 -
Rwork0.205 2632 -
all-2773 -
obs--95.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.00570.0355-0.27170.47920.00611.20670.0338-0.03920.01040.0166-0.0088-0.03230.010.0267-0.0250.0087-0.00540.00620.0051-0.01130.0816.92073.545929.4144
20.6170.1755-0.24370.32690.08681.3106-0.0070.00690.0428-00.00860.02710.0308-0.032-0.00160.0135-0.0033-0.00180.0027-0.00810.08257.69840.11643.2731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 207
2X-RAY DIFFRACTION2B1 - 203

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