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- PDB-5yii: Crystal Structure of 45 amino acid deleted from N-terminal of Pho... -

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Basic information

Entry
Database: PDB / ID: 5yii
TitleCrystal Structure of 45 amino acid deleted from N-terminal of Phosphoserine Aminotransferase (PSAT) of Entamoeba histolytica
ComponentsPhosphoserine aminotransferasePhosphoserine transaminase
KeywordsTRANSFERASE / Delta45_EhPSAT
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / L-serine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Phosphoserine aminotransferase / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Phosphoserine aminotransferase / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / phosphoserine transaminase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSingh, R.K. / Gourinath, S.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica.
Authors: Singh, R.K. / Tomar, P. / Dharavath, S. / Kumar, S. / Gourinath, S.
History
DepositionOct 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6862
Polymers35,6281
Non-polymers581
Water1,56787
1
A: Phosphoserine aminotransferase
hetero molecules

A: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3734
Polymers71,2572
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area3020 Å2
ΔGint-30 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.256, 103.044, 80.830
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 aminotransferase / Phosphoserine transaminase / Phosphoserine aminotransferase / putative


Mass: 35628.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EhPSAT, EHI_026360 / Plasmid: pET21C / Production host: Escherichia coli (E. coli) / References: UniProt: Q60I38, phosphoserine transaminase
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 2000MME, 100 mM potassium thiocyanate (KSCN)

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 30, 2015
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 54165 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 41.93
Reflection shellResolution: 1.8→1.83 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YB0

5yb0


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.51 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.154
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 1417 5.1 %RANDOM
Rwork0.229 ---
obs0.2311 54165 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 231.05 Å2 / Biso mean: 38.607 Å2 / Biso min: 19.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å2-0 Å2
2---0.77 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 3 87 2567
Biso mean--36.81 35.36 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192523
X-RAY DIFFRACTIONr_bond_other_d0.0010.022494
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9683400
X-RAY DIFFRACTIONr_angle_other_deg0.935751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.215310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88725.185108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54315484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.403159
X-RAY DIFFRACTIONr_chiral_restr0.1110.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02547
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 113 -
Rwork0.27 1964 -
all-2077 -
obs--100 %

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