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- PDB-8i28: Structure of Phosphoserine Aminotransferase from Saccharomyces ce... -

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Basic information

Entry
Database: PDB / ID: 8i28
TitleStructure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae
ComponentsPhosphoserine aminotransferase
KeywordsTRANSFERASE / Phosphoserine
Function / homology
Function and homology information


Serine biosynthesis / serine family amino acid biosynthetic process / phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / purine nucleobase biosynthetic process / L-serine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Phosphoserine aminotransferase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Phosphoserine aminotransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJang, J.Y. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2023
Title: Molecular Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae.
Authors: Jang, J. / Chang, J.H.
History
DepositionJan 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoserine aminotransferase
B: Phosphoserine aminotransferase


Theoretical massNumber of molelcules
Total (without water)86,9412
Polymers86,9412
Non-polymers00
Water95553
1
A: Phosphoserine aminotransferase

B: Phosphoserine aminotransferase


Theoretical massNumber of molelcules
Total (without water)86,9412
Polymers86,9412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_656y+1,x,-z+11
Buried area2030 Å2
ΔGint-14 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.278, 132.278, 141.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phosphoserine aminotransferase / PSAT / Phosphohydroxythreonine aminotransferase


Mass: 43470.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SER1, SERC, YOR184W / Production host: Escherichia coli (E. coli) / References: UniProt: P33330, phosphoserine transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.4 M ammonium sulfate and 0.1 M citric acid (pH 3.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35761 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 18.75
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 3519 / CC1/2: 0.506

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CZX

6czx


Resolution: 2.8→48.33 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 1995 5.59 %
Rwork0.2287 --
obs0.2309 35712 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 0 53 5253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015304
X-RAY DIFFRACTIONf_angle_d1.0947174
X-RAY DIFFRACTIONf_dihedral_angle_d6.631700
X-RAY DIFFRACTIONf_chiral_restr0.056812
X-RAY DIFFRACTIONf_plane_restr0.007918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.36461350.32642372X-RAY DIFFRACTION99
2.87-2.950.32831440.31032377X-RAY DIFFRACTION100
2.95-3.030.36181400.31382365X-RAY DIFFRACTION100
3.03-3.130.34741440.28322383X-RAY DIFFRACTION100
3.13-3.240.34751430.26982378X-RAY DIFFRACTION100
3.24-3.370.33281400.25742397X-RAY DIFFRACTION100
3.37-3.530.2431410.23322409X-RAY DIFFRACTION100
3.53-3.710.25771400.2162376X-RAY DIFFRACTION100
3.71-3.940.23111450.20872395X-RAY DIFFRACTION100
3.95-4.250.25651400.19292412X-RAY DIFFRACTION100
4.25-4.680.23631420.18772415X-RAY DIFFRACTION100
4.68-5.350.2141440.18542438X-RAY DIFFRACTION100
5.35-6.740.2431500.23452462X-RAY DIFFRACTION100
6.74-48.330.25931470.21612538X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 74.7884 Å / Origin y: 34.3092 Å / Origin z: 71.4581 Å
111213212223313233
T0.2419 Å20.1019 Å2-0.043 Å2-0.2508 Å2-0.0316 Å2--0.2576 Å2
L0.2606 °20.2389 °2-0.1904 °2-0.502 °2-0.4609 °2--0.4377 °2
S-0.0759 Å °0.2104 Å °-0.0285 Å °0.1768 Å °0.1477 Å °-0.0526 Å °0.0461 Å °0.0628 Å °0.0305 Å °
Refinement TLS groupSelection details: all

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